Cancer treatment with retroviral vectors comprising wild-type p53

ABSTRACT

Disclosed are methods and compositions for the selective manipulation of gene expression through the preparation of retroviral expression vectors for expressing antisense sequences, such as K-ras oncogene antisense sequences, or sequences encoding a desired product, such as wild type p53 sequences. Preferred retroviral vectors of the present invention incorporate the β-actin promoter in a reverse orientation with respect to retroviral transcription. Preferred antisense RNA constructs of the present invention employ the use of antisense intron DNA corresponding to distinct intron regions of the gene whose expression is targeted for down-regulation. In an exemplary embodiment, a human lung cancer cell line (NCI-H460a) with a homozygous spontaneous K-ras mutation was transfected with a recombinant plasmid that synthesizes a genomic segment of K-ras in antisense orientation. Translation of the mutated K-ras mRNA was specifically inhibited, whereas expression of H-ras and N-ras was unchanged. A three-fold growth inhibition occurred in H460a cells when expression of the mutated ras p21 protein was down-regulated by antisense RNA and cells remained viable. The growth of H460a tumors in nu/nu mice was substantially reduced by expressed K-ras antisense RNA.

The present application is a continuation application of U.S. Ser. No.07/960,513, filed Oct. 13, 1992, now U.S. Pat. No. 6,017,524 which is acontinuation-in-part of U.S. Ser. No. 07/665,538, filed Mar. 6, 1991,now abandoned.

The government may own certain rights in the present invention pursuantto NIH grants RO1 CA 45187 and CA 16672.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to methods and nucleic acid vectorcompositions for modifying gene expressing, involving the preparationand use of improved retroviral vectors which encode antisense RNAmolecules or, alternatively, transcriptionally active RNAs that encodeselected proteins. The retroviral constructs of the present inventionmay be employed for introducing desired gene expression units intoselected target cells, such as into tumor cells within individualsafflicted with cancer.

2. Description of the Related Art

It is now well established that a variety of diseases, ranging fromcertain cancers to various genetic defects, are caused, at least inpart, by genetic abnormalities that result in either the over expressionof one or more genes, or the expression of an abnormal or mutant gene orgenes. For example, many forms of cancer in man are now known to be theresult of, at least indirectly, the expression of “oncogenes”. Oncogenesare genetically altered genes whose altered expression product somehowdisrupts normal cellular function or control (Spandidos, et al., 1989).

Most oncogenes studied to date have been found to be “activated” as theresult of a mutation, often a point mutation, in the coding region of anormal cellular gene or of a “protooncogene”, that results in amino acidsubstitutions in the protein expression product. This altered expressionproduct, in turn, exhibits an abnormal biological function that somehowtakes part in the neoplastic process (Travali, et al., 1990). Theunderlying mutations can arise by various means, such as by chemicalmutagenesis or ionizing radiation.

A number of oncogenes have now been identified and characterized tovarying degrees, including ras, myc, neu, raf, erb, src, fms, jun andabl (Travali, et al., 1990; Minna, 1989; Bishop, 1987). It is likelythat as our knowledge of tumori-genesis increases, additional oncogeneswill be identified and characterized. Many of the foregoing, includingras, myc and erbB, comprise families of genes, whose expression productbear sequence similarities to other members of the family (Shih, et al.,1984; Bos, 1989; Schwab, et al., 1985). In the case of many of thesegene families, it is typical that oncogenesis involves an activation ofonly one member of the family, with other “unactivated” members servinga role in normal cellular functions (Id.).

The study of DNA-mediated gene transfer has revealed the existence ofactivated cellular oncogenes in a variety of human tumors (for review,see Cooper, et al., 1982). Oncogenes have been identified in humanbladder, colon, lung and mammary carcinoma cell lines (Krontiris, etal., 1981; Murray, et al., 1981; Perucho, et al., 1981), promyelocyticleukemia (Murray, et al., 1981), neuroblastoma (Shimizu, et al., 1983)and sarcoma cell lines (Pulciani, et al., 1982), and various solidtumors including carcinomas of the lung, and pancreas (Pulciani, et al.,1982). Studies have demonstrated that various transforming genesdetected by transfection correspond to activated cellular homologues ofretroviral oncogenes (Pulciani, et al., 1982; Der, et al., 1982; Parada,et al., 1982; Santos, et al., 1982), although others have no knownretroviral cognate (Tulciani, et al., 1982; Lane, et al., 1982).

The ras oncogene family has been perhaps the best characterized to date(Barbacid, 1987; Bos, 1989). Most of the identified transforming genesin human carcinomas have been a member of the ras gene family, whichencode immunologically related proteins having a molecular weight of21,000 (p21) (Ellis, et al., 1981; Papageorge, et al., 1982). Thisfamily is comprised of at least 3 members, one transduces as H-ras inthe Harvey strain of murine sarcoma virus (Ellis, et al., 1981), one asK-ras and Kirsten murine sarcoma virus (Ellis, et al., 1981), and oneidentified by low stringency hybridization to H-ras, termed N-ras(Shimizu, et al., 1983). As noted, all members of the ras gene familyencode closely related proteins of approximately 21,000 Daltons whichhave been designated p21s (Ellis, et al, 1981). The level of p21expression is similar in many different human tumor cells, independentof whether the cell contains an activated ras gene detectable bytransfection.

Nucleotide sequence analysis of the H-ras transforming gene of the EJhuman bladder carcinoma has indicated that the transforming activity ofthis gene is a consequence of a point mutation altering amino acid 12 ofp21 from glycine to valine (Tabin, et al., 1982). Studies of proteinsencoded by K-ras genes activated in four human lung and colon carcinomacell lines indicated that the transforming activity of K-ras in thesehuman tumors was also a consequence of structural mutations (Der andCooper, 1983). Other mutations have been found to result in ras geneactivation as well. For example, the H-ras gene activated in a lungcarcinoma cell line encodes the normal amino acid position 12 but ismutated at codon 61 to encode leucine rather than glutamine (Yuasa, etal., 1983). An N-ras gene activated in a human neuroblastoma cell lineis also mutated at codon 61 but encodes lysine rather that glutamine(Taparowski, et al., 1983). Thus, studies such as these have indicatedthat ras genes in human neoplasms are commonly activated by structuralmutations, often point mutations, that thus far occur at codon 12 or 61with different amino acid substitutions resulting in ras gene activationin different tumors.

Antisense RNA technology has been developed as one approach toinhibiting gene expression, particularly oncogene expression. An“antisense” RNA molecule is one which contains the complement of, andcan therefore hybridize with, protein-encoding RNAs of the cell. It isbelieved that the hybridization of antisense RNA to its cellular RNAcomplement can prevent expression of the cellular RNA, perhaps bylimiting its translatability. While various studies have involved theprocessing of RNA or direct introduction of antisense RNAoligonucleotides to cells for the inhibition of gene expression (Brown,et al., 1989; Wickstrom, et al., 1988; Smith, et al., 1986; Buvoli, etal., 1987), the more common means of cellular introduction of antisenseRNAs has been through the construction of recombinant vectors which willexpress antisense RNA once the vector is introduced into the cell.

A principal application of antisense RNA technology has been inconnection with attempts to affect the expression of specific genes. Forexample, Delauney, et al. have reported the use antisense transcripts toinhibit gene expression in transgenic plants (Delauney, et al., 1988).These authors report the down-regulation of chloramphenicol acetyltransferase activity in tobacco plants transformed with CAT sequencesthrough the application of antisense technology.

Antisense technology has also been applied in attempts to inhibit theexpression of various oncogenes. For example, Kasid, et al., 1989,report the preparation of recombinant vector construct employing Craf-1cDNA fragments in an antisense orientation, brought under the control ofan adenovirus 2 late promoter. These authors report that theintroduction of this recombinant construct into a human squamouscarcinoma resulted in a greatly reduced tumorigenic potential relativeto cells transfected with control sense transfectants. Similarly,Prochownik, et al., 1988, have reported the use of Cmyc antisenseconstructs to accelerate differentiation and inhibit G₁ progression inFriend Murine Erythroleukemia cells. In contrast, Khokha, et al., 1989,discloses the use of antisense RNAs to confer oncogenicity on 3T3 cells,through the use of antisense RNA to reduce murine tissue inhibitor ormetalloproteinases levels.

Unfortunately, the use of current antisense technology often results infailure, particularly where one seeks to selectively inhibit a member ofa gene family. One reason for this failure can be traced to the highexpression levels of antisense message that are apparently required forinhibition. Unfortunately, the requisite expression levels of antisensemessage has not been generally achievable with existing constructs.Problems have also arisen due to the similarity in underlying DNAsequences, which results in the cross-hybridization of antisense RNA,retarding the expression of genes required for normal cellularfunctions. An example is presented by Debus, et al., 1990, who reportedthat in the case of ras oncogenes, antisense ras oligonucleotides killboth normal and cancer cells, which, of course, is not a desired effect.

Another important “oncogene” is the gene encoding the p53 cellularprotein. The p53 gene is one of the most common targets for geneticabnormalities in human tumors (Hollstein et al., 1991). For example, ithas been reported that p53 mutations occur in all histological types oflung cancer at frequencies of about 75% in small cell lung cancer (SCLC)and about 50% in non small cell lung cancer (NSCLC) (Takahashi et al.,1991). Evidence suggests that p53 acts as a “tumor suppressor” gene, andits inactivation through mutation can lead to oncogenic development. Infact, a predominance of G to T transversions in p53 and ras mutations inlung cancer, as well as epidemiological data, supports a closeassociation between smoking and p53 mutations in NSCLC have suggestedthat p53 is a candidate for molecular targets of genetic damage causedby cigarette smoke (Zakut-Houri et al., 1985).

One approach that has been suggested as a means of treatment of suchtumors is the introduction of so-called “wild-type” or non-mutated p53(wt-p53) into affected cells, e.g., through the use of retroviralvectors which encode the wild type protein (Takahashi et al., 1992; Leeet al., EP appl. publ. 0 475 623 A1). The vectors proposed by theseindividuals included a wt-p53 genes wherein the direction oftranscription of the encoded wt-p53 was in the same orientation as thatof the retroviral long terminal repeats (LTRs). Unfortunately, instudies conducted by the present inventors reported hereinbelow, theability of retroviral wt-p53 constructs prepared having such anorientation to suppress tumor growth was found to be less than optimal.Presumably, this shortcoming is the result of poor expression of thewt-p53 gene in the target cells.

Therefore, while it is clear that current gene therapy technology showspotential promise as a means of external control of gene expression, itis equally clear that it does suffer particular draw backs, such as theneed for high level expression and a lack of selectivity where genefamilies are concerned. There is a particular need, therefore, for ageneral approach to the design of gene therapy protocols that will allowselective inhibition of gene expression, even in the case of closelyrelated genes.

SUMMARY OF THE INVENTION

The present invention, in a general and overall sense, addresses one ormore of the foregoing or other shortcomings in the prior art byproviding a novel approach to the design of retroviral vectors for theintracellular delivery of selected genetic constructs in a manner whichallows their use to inhibit the expression of specific genes, or toreplace defective genes, in target cells.

The inventors believe that the approach offered by the present inventionoffers more specificity and selectivity than previous approaches.Additionally, it is proposed that the present invention will allow thatthe development of vector technology for gene therapy having a muchimproved ability to inhibit or provide for specific gene expression,particularly in those instances where one desires to selectively inhibita particular gene over that of closely related genes or other members ofa gene family, or where one desires to provide for the expression of aspecific gene.

A particularly surprising aspect of the invention, discussed in moredetail below, is the finding that by aligning the selected promoter/geneconstruct within the vector in an orientation that is reversed withrespect to the direction of transcription of other promoters within thevector, one can achieve a dramatic increase in transcription of theintroduced gene. Thus, where retroviral vectors are employed, thepromoter/gene construct should be aligned so as to effect transcriptionin a direction that is opposite that of usual viral transcription. Inthe case of retroviruses, a reverse orientation is one that is oppositethat of long terminal repeat transcription. While this affect wasobserved using the β-actin promoter and a retroviral expression vector,the inventors believe that this phenomenon will be applicable to otherpromoter/vector constructs for application in gene therapy.

In one specific embodiment, the invention concerns vector constructs forintroducing wild type p53 genes (wt-p53) into affected target cellssuspected of having mutant p53 genes. These embodiments involve thepreparation of a gene expression unit wherein the wt-p53 gene is placedunder the control of the β-actin promoter, and the unit is positioned ina reverse orientation into a retroviral vector.

While aspects of the invention are exemplified through the use of wt-p53constructs, and their use in cancer treatment, it is proposed that theinvention is generally applicable to any situation where one desires toachieve high level expression of a recombinant protein in a target orhost cell through the use of a retroviral expression vector. This could,for example, involve the use of a gene encoding a recombinant proteinthat confers a particular trait, such as the use of wt-p53 to “replace”a trait that has been lost due to mutation, or could be used tointroduce protein-encoding genes that one desires to use for preparingproteins for other purposes, such as in recombinant protein productionprocedures. While the nature of the gene introduced is not critical tobroader aspects of the invention, it should be mentioned that in thecontext of cancer treatment modalities, a particular example in additionto p53 replacement that is contemplated by the inventors is theintroduction of the retinoblastoma gene (rb).

In embodiments where inhibition or suppression of gene expression isdesired, antisense molecules will be employed. By preparing a constructthat encodes an RNA molecule that is in antisense or “complementary”configuration with respect to the RNA readouts of the target gene, theconstruct will act to inhibit or suppress the ultimate expression of thetarget gene, presumably by binding to the target RNA and therebypreventing its translation. In that the novel aspects of this part ofthe invention concerns the discovery of an improved retroviral promoterconstruct, the invention is generally applicable to any antisenseconstruct.

For certain applications in the context of antisense constructs,therefore, the antisense RNA that is produced will be complementary to aselected cellular gene, such as an oncogene sequence or some othersequence whose expression one seeks to diminish through antisenseapplication. While all or part of the coding sequence may be employed inthe context of antisense construction, the inventors have found thatparticular advantage may be taken where one employs in the antisenseconstruct an intron-complementary region that will bind to transcribedintrons contained in the targeted RNA. It has been found that the use ofintron-complementary regions not only improves the inherent inhibitorycharacteristics of the antisense molecule, but it also provides one theability to selectively inhibit one member of a gene family over another.This is due to the fact that while exon regions of members of genefamilies will often be similar, it is typically the case that the intronregions of these genes will be different.

Thus, in preferred aspects of the invention, antisense molecules willinclude a region that is complementary to and is capable of hybridizingwith an intron region of the gene whose expression is to be inhibited.The inclusion of intron-complementary regions in the antisense RNAconstructs of the present invention is believed to be the key to both animproved inhibitory capability as well as selectivity. By way of theory,it is proposed that the use of antisense intron regions provides animproved capability for at least two reasons. It is known that thestructure of intron RNA plays a role in RNA processing.

The inventors propose that antisense introns bind to “sense” intronregions found on the initial RNA transcript of the gene, and affectsproper RNA processing. Thus, subsequent translation of protein-codingRNAs into their corresponding proteins is retarded or prevented. The useof antisense introns are believed to provide selectivity of inhibitionbecause the exon or “amino acid encoding” region of RNAs coding forclosely related proteins are often themselves closely related. This maynot be the case for the introns of closely related genes. Thus, whereintron regions between two genes are distinct, antisense introns can bedesigned which will hybridize selectively to a selected gene familymember, and not to other family members, and thereby inhibitselectivity.

As used herein, the term “intron” is intended to refer to gene regionsthat are transcribed into RNA molecules, but processed out of the RNAbefore the RNA is translated into a protein. In contrast, “exon” regionsof genes are those regions which are transcribed into RNA andsubsequently translated into proteins.

Thus, where one seeks to selectively inhibit a particular gene or genesover a related gene or genes, the inventors propose the preparation anduse of antisense RNA molecules which encode an intron region or regionsof the gene which one desires to inhibit selectively, that is distinctfrom intron regions of genes which one desires to leave unaffected. A“distinct” intron region, as used herein, is intended to refer to anintron region that is sufficiently different from an intron region ofanother gene such that no cross hybridization would occur underphysiologic conditions. Typically, where one intron exhibits a sequencehomology of no more than 20% with respect to a second intron, one wouldnot expect hybridization to occur between antisense and sense intronsunder physiologic conditions.

While it is generally preferred that antisense introns be prepared to becomplementary to an entire intron of the gene to be inhibited, it isbelieved that shorter regions of complementarity can be employed, solong as the antisense construct can be shown in vitro to inhibitexpression of the targeted expression product. The inventors believethat the most important intron regions in terms of the preparation ofantisense introns will be those regions closest to intron/exonjunctions. This is the region where RNA processing takes place. Thus, itis proposed that one will desire to include it in the antisense intronsufficient complementarity with regions within 50–100 nucleotides of theintron/exon junction.

The inventors have found that some antisense exon sequences of thetargeted gene can also be included in the antisense constructs of thepresent invention, so long as the resultant construct maintains itsselectivity, and will not seriously inhibit genes whose continuedfunction is relied upon by the cell for normal cellular activities. Theamount of antisense exon sequence included within the antisenseconstruct which can be tolerated will likely vary, depending on theparticular application envisioned. For example, antisense constructs fordown-regulation of K-ras expression have been prepared which includesequences complementary to exons II and III and all of intron II of theK-ras gene. These constructs contain antisense sequences to intron II ofK-ras, and selectively inhibit K-ras expression relative to H-ras orN-ras. Thus, in this instance, the inclusion of sequences complementaryto exons II and III of K-ras apparently did not result in thesignificant inhibition of the H-ras or N-ras genes, even though a 300nucleotide region of complementarity existed with exons of theunaffected genes.

One can readily test whether too much antisense exon DNA has beenincluded in antisense intron constructs of the present invention bysimply testing the constructs in vitro to determine whether normalcellular function is affected or whether the expression of related geneshaving complementary sequences are affected.

In connection with these aspects of the invention, it is proposed thatthe antisense constructs of the present invention, whether they be theantisense RNA molecules (i.e., oligonucleotides) or nucleic acidmolecules which encode for antisense RNA molecules, will have theirprincipal application in connection with the down-regulation of oncogeneexpression.

The most preferred oncogenes for application of the present inventionwill be those which exist as a family of genes, where one desires toselectively inhibit one member of a family over other members. In thisregard, one may mention by way of example, the ras, myc, erb or junfamilies of oncogenes. Certain of these, such as the ras family,involves the activation of protooncogenes by a point mutation, whichapparently results in the expression of a biologically abnormal product.

In aspects that relate to the use of intron sequences, the presentinvention contemplates that antisense intron RNA can either be applieddirectly to cells, in the form of oligonucleotides incorporatingantisense intron sequences, or by introducing into the cell nucleic acidsequences that will encode the desired antisense construct in the formof retroviral constructs. In the former case, it has been shown byothers that antisense oligonucleotides can successfully traversecellular membranes. The present inventors envision that such an approachmay be an option to therapy, particularly where the antisenseoligonucleotides are successfully packaged to maintain their stabilityin circulation, for example, by liposome encapsulation.

Other techniques for direct insertion in the cells include, by way ofexample, electroporation, or calcium phosphate transfection.Furthermore, where one desires to treat conditions of the bone marrow,bone marrow cells can be successfully removed from the body, treatedwith antisense constructs, and replaced into the body similar to theadoptive immunotherapy approach employed in IL-2 treatment.

In broader aspects of the invention, a preferred approach will involvethe preparation of retroviral vectors which incorporate nucleic acidsequences encoding the desired construct, once introduced into the cellsto be treated, preferably, these sequences are stably integrated intothe genome of the cell. One example of such of vector construct would bea replication defective retrovirus, such as LNSX, LN or N2A, that ismade infective by appropriate packaging, such as by GPtenvAM-12 cells.Although the retrovirus would inhibit the growth of the tumor, theexpression of the antisense construct in non-tumor cells would beessentially harmless where one prepares a retrovirus construct whichencode distinct antisense intron RNA in accordance with the presentinvention. In addition to retroviruses, it is contemplated that othervectors can be employed, including adenovirus, adeno-associated virus,or vaccinia viruses (Hermonat, et al., 1984; Karlsson, et al., 1985;Mason, et al., 1990).

The particular promoter that is employed to control the expression ofthe antisense RNA in a vector construct is not believed to beparticularly crucial, so long as it is capable of expressing theantisense intron RNA in the targeted cell of a rate greater than 5 foldthat of the gene to be inhibited. Thus, where a human cell is targeted,it will be preferred to position the antisense RNA coding regionadjacent to and under the control of a promoter that is capable of beingexpressed in a human cell. Generally speaking, such a promoter mightinclude either a human cellular or viral promoter. While the β-actinpromoter is preferred the invention is by no means limited to thispromoter, and one may also mention by way of example promoters derivedfrom RSV, N2A, LN, LNSX, LNSN, SV40, LNCX or CMV (Miller, et al., 1989;Hamtzoponlos, et al., 1989).

The most preferred promoters will be those that are capable of beingexpressed in a wide variety of histologic cell types, and which iscapable of continuously expressing the antisense RNA. A preferredexample is the β-actin promoter, because the promoter functionseffectively in human epithelial cells. Other examples of promotershaving a similar capability include RSV and SV40.

Where retroviral vectors are concerned, a more particular feature of thepresent invention is the general, overall design of preferred retroviralvector constructs. The most preferred vector design of the presentinvention takes into account the inventors' discovery that when aparticular promoter, the β-actin promoter, is employed to driveexpression of a selected gene, and the expression construct ispositioned in an orientation that is opposite that of retroviraltranscription, there is a surprising increase in the relative expressionof the selected gene. Thus, generally speaking, retroviral constructs ofthe present invention can be said to include a gene expression unitwhich includes a selected gene under the control of a β-actin promoter,wherein the gene expression unit is positioned to effect transcriptionof the selected gene in an orientation opposite that of retroviraltranscription.

By “reverse orientation” or “opposite orientation” is meant that theorientation of transcription of the selected gene that is under thecontrol of the β-actin promoter is in the opposite direction from thedirection of transcription of the regular retroviral genes. Thus, forexample, where the vector includes a long terminal repeat (LTR), as domost retroviral vectors, the orientation of transcription of theselected gene will be opposite that of the LTR.

While the retroviral construct aspect of the present invention concernsthe use of a β-actin promoter in reverse orientation, there is nolimitation on the nature of the selected gene which one desires to haveexpressed. Thus, the invention concerns the use of antisense-encodingconstructs as well as “sense” constructs that encode a desired protein.

Of particular importance is the inventors somewhat surprising discoverythat reversing the orientation of the genetic construct with respect tothe direction of transcription of the retroviral vector dramaticallyimproves expression of the selected gene. This effect is dramaticallyillustrated in the context of K-ras antisense therapy (see FIG. 9A andExample II below). In these studies, when the antisense construct wasexpressed from a retroviral vector aligned in the same direction oftranscription as the retroviral LTR, the effect in suppressing targetcells versus control cell growth was evident, but target cells growthwas nonetheless observed by 7 days. In stark contrast, no growth wasobserved after 7 days where the reverse orientation construct wasemployed.

The nature of the retroviral vector that is employed may depend upon theapplication that is envisioned. For clinical application, there areseveral types of such vectors that have been found or proposed asapplicable, such as a Moloney murine leukemia virus vector, mousemammary tumor virus, or related retroviruses, or the like. The use ofthese vectors for clinical applicable rests upon the fact that they donot include active viral genes that could be considered harmful tohumans or animals and do not lead to the production of infective virusesupon infection. However, the invention is not limited in its scope toclinical applications, and for applications that do not contemplateclinical administration to humans or animals it is proposed thatvirtually any type of retrovirus can be employed.

Certain preferred vectors designed and employed by the present inventorswill include a second gene expression unit which includes a second gene,such as a selectable marker gene, expressed from a retroviral long-termrepeat. The presence of a selectable marker genes facilitate thepreparation of the vector by allowing the selection of appropriate hostcells from which the vector is prepared. The nature of the marker geneis not believed to be particularly crucial, so long as it does notproduce a product that is harmful to the host cell, or to humans oranimals where clinical application is contemplated.

Where clinical application of retroviral vectors is contemplated, itwill be necessary to prepare the vector and place it into apharmaceutical composition that is appropriate for the intendedapplication. This will entail generally preparing a pharmaceuticalcomposition that is essentially free of pyrogens, as well as any otherimpurities that could be harmful to humans or animals. One will alsogenerally desire to employ appropriate salts and buffers to render thevector stable and allow for vector uptake by target cells. Thepreparation of appropriate pharmaceutical retroviral compositions aregenerally well known, as are appropriate amounts, etc., of vectors to beemployed.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 A) The second exon of the K-ras gene was amplified from genomicDNA of H522, H322, Calu 1, H226, H460a and human placenta by polymerasechain reaction (PCR), blotted onto a gene screen membrane and hybridizedwith ³²P end-labeled oligonucleotide probes. FIG. A1 shows the presenceof wild-type glutamine residue (CAA) at 61 codon in five cell linesexcept H460a. The same blot was reprobed with a histidine-specificmutated oligo probe (CAT) and only the H460a cell line PCR DNAhybridized (FIG. A2). The mutation was confirmed by direct PCR DNAsequencing. Wild-type K-ras 61 codon sequence in human placenta (FIG.A3) was compared with the H460a cell line (FIG. A4).

B) A 2 kb genomic DNA segment from the K-ras oncogene was subcloned intoin Apr-1-neo vector in both a sense and antisense orientation. A 2 kbEco RI/Pst I fragment containing second and third exon sequencestogether with adjoining flanking intron sequences was isolated from theSP6 vector (Oncogene Sciences) and Klenow enzyme was used to make bluntends. Apr-1-neo vector was digested with Bam HI and blunt end ligationwas performed to obtain the Apr-1-neo AS or Apr-1-neo A constructs.

C) A southern blot analysis of the K-ras oncogene in H460a and H460atransfectants. Blots were probed with P32 nick translated 2 kb EcoR1/Pst1 insert DNA. 1) H460a, (2,3) H460a transfected with Apr-1-neo SC₁#1 and C₂#1 (4,5) H460a cells transfected with Apr-1-neo AS, C₃#32 andC₂#32, respectively.

D) A northern blot analysis of sense and antisense K-ras RNA. 1)H460a,(2,3) Apr-1-neo S transfectants, (4,5) Apr-1-neo AS transfected clones.

E,F) A Western blot analysis of K-ras specific p21-protein (1E) andtotal ras protein (1F) was performed using either pan ras or K-rasspecific monoclonal antibodies. 1) Calu-1 control cell line overexpressing K-ras specific protein. 2) H460a; 3) H460a Apr-1-neo S; 4,5)H460a Apr-1-neo AS.

G) Map of plasmid pH β APr-1-neo

FIG. 2 A) Schematic diagram of K-ras RNA synthesis. A segment of rascDNA was amplified using oligonucleotide primers corresponding to the 5′region of first exon and 3′ of second exon (indicated by arrows) for RNAPCR analysis.

B) An RNA PCR analysis was done to compare the level of K-ras message inH460a and H460a transfectants. As a control, a portion of p53 gene wasco-amplified with p53 specific primer which served as an internalcontrol.

C,D) H-ras and N-ras specific amplimers were used to quantitateH-ras/N-ras RNA in the transfectants and parental cell lines. p53 geneamplification is shown as an internal control.

FIG. 3 (A) In vitro growth curve. Cells were seeded at 10⁴ cells/plateand grown for a seven day period. Cells were harvested and counted in ahemocytometer at 24 h intervals. Growth curves for H460A and H460A cellstransfected with Apr-1-neo S vector do not show any significantdifference, but H460A transfectants carrying Apr-1-neo-AS showed growthinhibition (Fig. B). Female BALB/C nu/nu mice were injected with 10⁶H460a cells subcutaneously in the left flank. Cross-sectional diametersof the external tumor were measured without knowledge of the cell group.Tumor volume was calculated by assuming a spherical shape with theaverage tumor diameter calculated as the square root of the product ofcross-sectional diameters. Palpable tumors were first detected on day15. Each point represents the mean±SE. C3#32-AS (n=5), C3#1-S (n=5),H460a (n=3). C3#32-AS was compared to C3#1-S or H460a on days 20, 25,30, 35 (p<0.05 by Wilcoxon's Test).

FIG. 4 Subcloning of β-actin K-ras antisense fragment in the LNSXretroviral vector. A 1.8-Kb genomic K-ras DNA segment with a 4-Kbβ-actin promoter in antisense orientation was subcloned into a 6-Kb LNSXretroviral vector using blunt (a) or Hind III linker (b) ligations intwo orientations.

FIG. 5 LNSX-antisense (a) retrovirus infection efficiency in H460acells. A. H460a cells 10⁵ in 6-well plates were infected once with 1 mlof each serial dilutions of retroviral stocks in the presence of 8 μg/mlpolybrene. Two days later, seeding equal numbers of H460a transducedcells into 300 μg/ml G418 selective medium or nonselective medium for10–14 d. Infection efficiency=(No. of colonies in G418 medium)/(No. ofcolonies in medium without G418). B. H460a cells 10⁴ in 12-well plateswere incubated with 0.5 ml LNSX-antisense (orientation a) retroviralstocks (Titer: 2×10⁶ CFU/ml). Polybrene 8 μg/ml was also added. Theinfections were done once each day for 1 to 7 d. Fresh medium andsupernatant were added at each time point. The infection efficiency wascalculated as for A.

FIG. 6 PCR analysis of transduced H460a cells. The genomic DNA of H460awas extracted and amplified by PCR with neo 1 and neo 5 oligonucleotideprimers. The PCR products were electrophoresed on 2% ethidiumbromide-stained agarose gel (A). The DNA was transferred ontonitrocellulose membranes and hybridized with ³²P-nick-translated neogene probe (B). Lane 1: molecular weight marker; Lane 2: H460a-antisenseLNSX (orientation a); Lane 3: H460a-antisense-LNSX (orientation b); Lane4: H460a-LNSX; Lane 5: parental H460a; Lane 6: LNSX vector plasmid DNA.

FIG. 7 Slot blot hybridization of poly(A+) RNA of H460a cells. Poly (A+)RNA was extracted, spotted onto nitrocellulose membranes (8 μg 4 μg, or2 μg) and hybridized with ³²P-end-labeled 42 bp K-ras exon 2 senseoligonucleotide probe (A). The filter was reprobed with a³²P-nick-translated β-actin probe to check for equal loading (B). Lane1: H460a-antisense-LNSX (orientation b); Lane 2: H460a-antisense-LNSX(orientation a); Lane 3: H460a-LNSX; Lane 4: H460a parental cells.

FIG. 8 Western blot analysis of ras p21 proteins in H460a cells. Onehundred micrograms of protein was size fractionated by 12.5%SDS-polyacrylamide gel and electroblotted onto nitrocellulose membranes.K-ras-p21-specific (A) and pan-ras-specific monoclonal antibodies (B)were used, followed by HRP-labeled goat anti-mouse second antibody. Lane1: H460a parental cells; Lane 2: H460a-LNSX; Lane 3:H460a-antisense-LNSX (orientation b); Lane 4: H460a-antisense-LNSX(orientation a).

FIG. 9 A. Growth curve of H460a cells in vitro. Cells 10³/well wereseeded in 12-well plates and grown for 7 days. Cells were harvested andcounted daily by trypan blue exclusion. B. Growth curve of MRC-9 cellsin vitro.

FIG. 10 Soft agarose colony formation of H460a cells. Cells 5×10⁴ weremixed with 0.35% agarose in RPMI 1640 route medium and plated over abase layer of 0.7% agarose and culture medium hardened in 60-mm dishes.Colonies were counted 10–14 d later. A: Parental H460a; B: H460a-LNSX;C: H460a-antisense-LNSX (orientation a); D: H460a-antisense-LNSX(orientation b).

FIG. 11 Functional transduction efficiency of LNSX-AS-K-ras in H460acells. Growth curves are shown for 10³ cells/well seeded in 12 wellplates. H460a cells were infected by incubation 0.5 m of viralsupernatant stock from either LNSX or LNSX-AS-K-ras (6×10⁶ CFU/ml) dailyfor 4 consecutive days in the presence of 8 μg/ml of polybrene. Theparental H460a cells served as a control. Cells were not selected withG418. Cells were counted daily. The mean±SE is shown for 3 replicates.

FIG. 12 H460a cells were infected with LNSX-AS-K-ras by incubating 10⁴cells with 0.5 ml of viral stock (6×10⁶ CFU/ml) produced by thepackaging cell line GP+envAm12 in the presence of 8 μg/ml of polybrene.Infection was done daily for 1 to 7 days. Two days later cells wereplated in equal numbers into selective media containing 200 μg/ml G418.Control H460a cells were plated at equal cell numbers to determinebaseline colony forming efficiency. The infection efficiency wasmeasured by determining the percent of the unselected colony numberformed by the G418 selected colonies.

FIG. 13 Growth curves are shown for 10⁴ cells/well seeded in 12 wellplates. H322a cells were infected by incubation 0.5 m of viralsupernatant stock from either LNSX, DC, LNSX-p53 or DC-p53 (10⁶ CFU/ml)on 2 consecutive days in the presence of 8 μg/ml of polybrene. Theparental H322a cells served as a control. Cells were not selected withG418. Cells were counted daily. The mean±SE is shown for threereplicates.

FIG. 14 Growth curves are shown for 10⁴ cells/well seeded in 12 wellplates. H460a cells were infected by incubation 0.5 m of viralsupernatant stock from either LNSX, DC, LNSX-p53 or DC-p53 (10⁶ CFU/ml)in the presence of 8 μg/ml of polybrene. The parental H322a cells servedas a control. Cells were not selected with G418. Cells were counteddaily. The mean±SE is shown for three replicates.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Molecular Events in Lung Cancer Development

Lung cancer remains the leading cause of cancer deaths in the UnitedStates where it kills more than 140,000 people annually. Recently,age-adjusted mortality from lung cancer has surpassed that from breastcancer in women. Although implementation of smoking-reduction programshas decreased the prevalence of smoking, lung cancer mortality rateswill remain high well into the 21st century (Brown et al., 1988).Unfortunately, all current treatment modalities, including radiationtherapy, surgery, and chemotherapy, have limited effectiveness. Therational development of new therapies for lung cancer will depend on anunderstanding of the biology of lung cancer at the molecular level.Research carried out in the laboratories of the present inventors hasidentified critical molecular events leading to NSCLC development andprogression. The goal of this research is to directly modify the cancercell to eliminate the expression of gene products which are responsiblefor the maintenance or progression of the malignant phenotype or torestore in normal form deleted or mutated gene products that suppressthe characteristics of the malignant phenotype.

The most common lung cancer histologies (80%) are grouped under the termnon-small-cell lung cancer (NSCLC) and include squamous, adenocarcinoma,and large-cell undifferentiated. Many of the current data on themolecular biology of lung cancer come from the study of the moreuncommon small-cell lung cancer (SCLC). SCLC can be distinguished fromNSCLC by the neuroendocrine features of the cells; SCLC is veryresponsive to chemotherapy but recurs rapidly after treatment. NSCLCalso may serve as a model for other carcinogen-induced epithelialcancers. The approaches and observations developed in this study may beapplicable to other types of epithelial cancers.

Abundant evidence has accumulated that the process of malignanttransformation is mediated by a genetic paradigm (Bishop et al., 1991).The major lesions detected in cancer cells occur in dominant oncogenesand tumor suppressor genes. Dominant oncogenes have alterations in aclass of genes called proto-oncogenes, which participate in criticalnormal cell functions, including signal transduction and transcription.Primary modifications in the dominant oncogenes that confer the abilityto transform include point mutations, translocations, rearrangements,and amplification. Tumor suppressor genes appear to require homozygousloss of function, by mutation, deletion, or a combination of these fortransformation to occur. Some tumor suppressor genes appear to play arole in the governance of proliferation by regulation of transcription.It is possible that modification of the expression of dominant and tumorsuppressor oncogenes may influence certain characteristics of cells thatcontribute to the malignant phenotype.

Despite increasing knowledge of the mechanisms involved inoncogene-mediated transformation, little progress has occurred indeveloping therapeutic strategies that specifically target oncogenes andtheir products. Initially, research in this area was focused on dominantoncogenes, as these were the first to be characterized. DNA-mediatedgene transfer studies showed acquisition of the malignant phenotype bynormal cells following the transfer of DNA from malignant human tumors.Activated oncogenes of the ras family were identified by this techniquewith transfection of human DNA into mouse NIH 3T3 cells.

Oncogene Mutations in Lung Cancer

Activation of the K-ras oncogene occurs in human NSCLC (Santos et al.,1989, Shimizu et al., 1983). Recent studies using the polymerase chainreaction (PCR) and specific oligonucleotide hybridization show that athird of NSCLC patients have ras family mutations (Rodenhuis et al.,1987; Rodenhuis et al., 1988). However, Reynolds and coworkers, using asensitive NIH 3T3 cotransfection-nude mouse tumorigenicity assay, foundthat 12 of 14 (86%) lung tumor DNAs from smokers contained activatedproto-oncogenes related to the ras family (Reynolds et al., 1991). K-rasmutations occur primarily in adenocarcinomas, and the K-rasproto-oncogene has a point mutation in 30% to 40% of adenocarcinomas ofthe lung (Rodenhuis et al., 1987; Rodenhuis et al., 1988). Thus, aminimum of 32,000 patients per year are expected to developras-mutation-positive lung cancer. K-ras mutations are associated with ahistory of tobacco consumption and may contribute to tumor progression.

The p53 gene is the most frequently mutated gene yet identified in humancancers. It is mutated in over 50% of human NSCLC (Hollestein et al.,1991). The p53 gene encodes a 375-amino-acid phosphoprotein that canform complexes with host proteins such as large-T antigen and E1B (Laneet al., 1990). Missense mutations are common for the p53 gene and areessential for the transforming ability of the oncogene. The wildtype p53gene may directly suppress uncontrolled cell growth or indirectlyactivate genes that suppress this growth. Thus, absence or inactivationof wildtype p53 may contribute to transformation. However, some studiesindicate that the presence of mutant p53 may be necessary for fullexpression of the transforming potential of the gene. Mutations of p53are common in a wide spectrum of tumors (Bressac et al., 1990; Dolcettiet al., 1990; Rodrigues et al., 1990; Nigro et al., 1989); they occur inboth NSCLC and SCLC cell lines and fresh tumors (Nigro et al., 1989;Takahashi et al., 1989).

Options for specific targeting of oncogenes include inhibition ofexpression of a dominant gene or replacement of a deleted or mutatedtumor suppressor gene. Progress in the understanding of the criticalgenes involved in tumor development and in technology for altering geneexpression logically led to our studies of techniques for achievingthese options. Initially, a model for specific inhibition of K-ras wasdeveloped. We chose to work with K-ras because of the applicability ofthe findings to a large number of tumors, because of our previous workwith K-ras, and because information on the genetic organization andsequence of the ras gene family was readily available. Advances inantisense and retroviral gene transfer technology suggested thatapplication of these techniques may mediate specific inhibition ofoncogene expression.

Antisense mRNA, which is precisely complementary to the correspondingsense mRNA, inhibits translation. The mechanisms for this inhibitionhave not been completely defined but include inhibition of translationby ribosomes, degradation of sense-antisense duplexes by enzymes, andfailure of export from the nucleus. Thus, specific targeting of a genein a multigene family could occur if it possessed unique sequences in aregion amenable to antisense inhibition, such as an initiation codon orsplice site.

The working hypothesis that was developed by the inventors is thatreversal of a single altered genetic event in the cancer cell canpotentially reverse critical features of the malignant phenotype of thatcell. This finding has important therapeutic implications. Cancer cellshave multiple genetic alterations. Therapy directed toward oncogeneswill be practical only if therapeutic effects occur with targeting ofone or two genes. It is unlikely that any therapy targeting oncogenes ortheir products will be absolutely specific for cancer cells. If othergenes can compensate for loss of normal function by a specific oncogenemediated by an antisense construct, the harmful effects of the therapywill be reduced.

Studies from the inventors' laboratory indicate that reversal of asingle genetic alteration has profound effects on the growth andtumorigenicity of lung cancer cells (Mukopadhyay et al., 1990;Mukopadhyay et al., 1991). Additional support for this concept comesfrom a recent study by Soriano and coworkers (Soriano et al., 1991) inwhich transgenic mice were created that lacked a functional c-srcproto-oncogene. The resulting developmental defect in the mice wasosteopetrosis. The ubiquity of c-src, its high degree of conservationamong species, and its role in mitosis suggest that inactivation wouldbe lethal, but this was not the case; viable mice were recovered. Apossible explanation is that other closely related nonreceptor tyrosinekinases such as yes and fyn can compensate for loss of c-src.Introduction of a single copy of a wildtype tumor suppressor gene intonormal cells would be unlikely to have adverse effects if it occurredduring therapy directed at replacing inactivated tumor suppressor genesin cancer cells.

Preliminary data on transfection of an antisense K-ras expression vectorindicated that inhibition of expression of a single oncogene reduced thegrowth rate of cancer cells and tumorigenicity in nu/nu mice. However,transfected cells retained viability, as did cells with no endogenousK-ras mutation that were also transfected with the construct. The wtp53appears dominant over the mutant gene and will select againstproliferation when transfected into cells with the mutant gene(Mukhopadhyay et al., 1991; Chen et al., 1990). Normal expression of thetransfected wtp53 does not affect the growth of cells with endogenouswtp53. Thus, such constructs might be taken up by normal cells withoutadverse effects.

Treatment Protocol Development

The inventors have developed a protocol for the treatment of tumorssusceptible to either wtp53 or antisense K-ras gene therapy. Thisprotocol focuses regional delivery of the two gene constructs, antisenseK-ras and wtp53, to lung cancer cells in patients with unresectableobstructing endobronchial cancers. The efficiency of delivery and geneexpression will be evaluated both in lung cancer cells and in normalcells in vivo. This is of importance for the design of constructs thatmay be useful therapeutically. The effects of these constructs onclinical progression of the cancer will be studied.

It is proposed that these approaches will lead to cancer therapy basedon direct alteration of gene expression in cancer cells. Current therapyrelies on attempts to kill or remove the last cancer cell. However,tumor cell dormancy is an established phenomenon making effectivekilling highly unlikely. Although inhibition of expression of someoncogenes may be lethal to the cancer cell, in some cases cellreplication will slow or cease, thus rendering these cancers clinicallydormant. Even if absolute specificity is not achieved, single oncogenesmay still be important targets, because it is likely that adverseeffects to normal cells will be minimal.

Natural History of Locally Unresectable NSCLC

Patients with NSCLC will die of their cancer in 86% of cases. Regionaldelivery of gene constructs to areas at risk for development of cancerhas important implications for both prevention and therapy. Failure oftherapy at the primary tumor site is a significant problem (Humphrey etal., 1990; Perez et al., 1990). Of the 161,000 patients newly diagnosedwith lung cancer in 1991, 45,080 will undergo surgical resection. Localrecurrence as the first site of failure will occur in 9,000 of thosepatients. Of the remaining patients, 52% will have localized tumors.However, 38% of these patients will have local failures followingradiation therapy (22,900). Thus, 31,900 patients per year could benefitfrom improved local-regional therapy. Patients with unresectableobstructing NSCLC that is resistant to radiation therapy or who havecoexisting metastases have a median survival of 6 months or less (Komakiet al., 1992).

Measure of Disease Activity

The ultimate goal of this therapy is to halt or reverse themanifestations of the disease. The efficacy of therapy in this group ofpatients will be measured by determining length of patient survival,length of time the affected lobe of the lung remains aerated, andreduction in measurable endobronchial tumor. There is no curativetherapy for this stage of disease and thus the outcome is predictableenough to allow for an assessment of the results of gene therapy.

Anticipated Effect of Protocol Treatment

It is anticipated that the uptake of the retroviral constructs byproliferating NSCLC cells will decrease the rate of proliferation ofthese cells. This would increase the length of time the affected lungwould remain expanded, prevent regrowth of the endobronchial tumor, andprolong the patient's survival.

Alternative Therapies

Patients with unresectable endobronchial tumor recurrence that ispartially or completely obstructing the airway and that have failed orare unable to receive external beam radiotherapy will be considered forthis protocol. Existing therapies for this condition offer onlyshort-term palliation. Most patients have recurred despite external beamradiotherapy. It may be possible to insert a brachytherapy catheter andadminister additional radiotherapy. Patients receiving this treatmenthave a median survival of 6 months (Komaki et al., 1992). Patientsfailing brachytherapy would also be eligible to receive gene therapy.Tumor can be removed from the airway with the laser or biopsy forceps.This can be done in conjunction with injection of the retroviralconstruct thus decreasing the volume that must be injected. Theadministration of the retroviral constructs would not preclude thepatient from receiving other palliative therapy if the tumor progresses.

Antisense Embodiments

As noted above, where one contemplates employing an antisense approachto selectively inhibit one of a family of genes, it will be particularlyadvantageous to include within the construct regions encoding anantisense intron region complementary to an intron unique to the targettranscript. In such circumstances, the present invention will begenerally applicable to the down-regulation of any gene which comprisesa distinct intron region, particularly those oncogenes which are membersof family wherein one desires to leave unaltered the expression of otherfamily members.

The present invention will have particular application to the selectiveinhibition of ras gene expression. For example, in the case of ras genetumorigenesis, only one of the various ras gene family members undergoesmutation-based protooncogene activation. The remaining, non-activatedras gene family member(s) serve useful cellular biological functions andare apparently required for normal cellular function. Thus, it isdesirable to specifically down-regulate the activated ras gene product,while leaving essentially unaffected, the non-activated ras genecounterparts. Thus, the present invention will have a particularapplication in the context of preferentially controlling ras geneexpressing.

While this aspect of the invention is exemplified in terms of thecontrol of ras gene expression, there is, of course, no reason why thepresent invention will not be similarly applicable to other genes andgene families, in light of the disclosure herein and the generalknowledge and skill in the art.

Generally speaking, to practice the antisense/intron aspects of thepresent invention in the context of the ras gene system it will be firstimportant to determine which of the various ras genes is involved in theoncogenic process to be retarded. This is a fairly straightforwardundertaking, and involves generally that one first obtain cells whichare expressing the activated ras gene product. To determine the natureof the activation, one then simply extracts DNA, amplifies the specificsequences of interest (see Table 1 below), and shows the presence orabsence of the mutation by either direct sequence analysis or specifichybridization with a known oligonucleotide sequence.

After the particular activated ras gene has been identified, anappropriate intron region is then selected for constructing theantisense construct. The most appropriate introns are those which havelittle or no homology to other known genes. In general, it will bepreferable to identify an appropriate intron structure for use inconnection with the present invention an analysis of the nucleicsequence of the intron, and comparison with selected that of introns ofother family members or related genes. The best choice of introns willbe those having 1) a different length from corresponding introns andsimilar location in other members of the gene family, and 2) little orno sequence homology with the introns of the other members.

An alternative, and sometimes simpler method to identify distinctintrons involves a comparison of sequence homologies can be ascertainedby cross-hybridization of introns from one family member with those ofother genes.

In any event, representative methods for cloning ras genes correspondingto the N-ras, K-ras and H-ras genes, have been described in theliterature (McGrath, et al., 1983; Shimizu, et al., 1983; Yamamoto, etal., 1985; Kraus, et al., 1984). These teachings should provide those ofskill in the art with adequate direction where one seeks to obtainsequences corresponding to the various ras gene intron.

A preferred method for cloning intron sequences is through theapplication of PCR-amplified cloning. In this relatively well knowntechnique, one employs oligonucleotide primers which allow the specificamplification of the desired intron region. The primer itselfcorresponds to exon sequences, in that these sequences will most likelybe generally available in the scientific literature for the particularapplication envisioned. Of course, where the intron sequences are known,computer assisted comparisons may be carried out to identify distinctregions, and appropriate PCR primers designed accordingly.

Recombinant clones which incorporate intron DNA are readily achievedthrough the PCR amplification of the distinct desires region usingprimers, e.g., that border the region, incorporating the amplified DNAinto a recombinant clone, and selecting recombinant clones which havereceived the intron DNA-bearing clones. The intron DNA containing clonesare then purified, and, preferably, the cloned DNA sequencedsufficiently to ensure that it contains the desired sequences.

Intron DNA is then removed from the vector employed for intron DNAcloning, and employed in the construction of appropriate antisensevectors. This will entail, of course, placing the intron DNA in anantisense direction behind an appropriate promoter and positioned so asto bring the expression of the antisense intron under control of thepromoter.

When selecting primers for intron sequence amplification, one willtypically desire to employ primers such that at least 50 and preferably100–200, nucleotides of the intron are amplified and thereby cloned. Ingeneral, it is believed that the larger the distinct antisense intronregion is, the better able it will be to selectively down-regulate thetargeted gene. Furthermore, it is believed that particular advantageswill be realized through the selection of intron regions which includeintron/exon boundaries, or simply just the intron side of theintron/exon boundaries. The reason for this is that RNA processing takesplace at the intron/exon boundary of the RNA and it is believed that theantisense intron DNA will have its greatest effect when targeted to thisjunction.

The particular vector which one employs for introduction of antisenseintron coding sequences is not believed to be particularly crucial tothe practice of the present invention, so long as the vector is capableof introducing the nucleic acid coding sequences into the genome of thetargeted cell in a relatively stable fashion. By way of illustration,but not limitation, one can mention the following vectors, includingN2A, LN, LNSX, Adenovirus and Adeno-associated virus.

The most preferred vector construct for targeting cells is the LNSXretroviral vector. This vector is based on the N2 vector, which containsthe extended packaging signal that allows for the production of thevector at a high titer. This vector was modified by inserting a stopcodon in place of the Pr65 gag start codon to prevent synthesis of Pr 65gag, and by replacing the upstream region of the vector with thehomologous region from Moloney murine sarcoma virus. These alterationsprevent synthesis of viral proteins from the vector. Splicing is notrequired for efficient neo-protein expression. The neo gene is expressedfrom the upstream LTR promoter.

The following examples are included to provide actual working protocolswhich the inventors have developed or adopted for carrying out preferredembodiments of the invention. Those of skill in the art will readilyappreciate that many of the techniques employed in the followingexamples are illustrative of standard laboratory practices, which havebeen found by the inventors to work well in the practice of theinvention. It will, however, be apparent to those of skill in the art,in light of the following examples, that numerous materials and/ormodifications and procedures and nevertheless achieve a useful result.

EXAMPLE I Specific Inhibition of K-ras Expression and Tumorigenicity ofLung Cancer Cells by Antisense RNA

A. Introduction

A wide spectrum of human cancers harbor ras genes activated by a singlepoint mutation (Barbacid, 1987; Rodenhuis, et al., 1987; Bos, 1989;Rodenhuis, et al., 1990; Mabry, et al., 1988; Santos, et al., 1984;Taya, et al., 1984; Cline, et al., 1987; Feig, et al., 1984; Vogelstein,et al., 1988; Kumar, et al., 1990). Despite considerable knowledge ofthe structural aspects of the ras gene product, the functional role inphysiological and pathological processes remains elusive (Barbacid,1987). Cellular location and structural and biochemical similarities toG proteins suggest that ras gene products are involved in signaltransduction (Bos, et al., 1987; Hurley, et al., 1984). The presentexample describes the preparation and use of an antisense RNA constructto block selectively the production of the mutated protein in the humannon-small cell lung cancer (NSCLC) cell line NCI-H460A. The directcontribution of the mutated p21 protein to the malignant phenotype wasalso examined.

B. Materials and Methods

H460, H322, H226, H522 non-small cell lung cancer (NSCLC) cell lineswere generously provided by Drs. J. D. Minna, A. F. Gazdar, NCI NavalMedical Oncology Branch, Bethesda, Md. All cell lines were grown inregular RPMI medium, 5% FCS, in routine culture.

1. Plasmid Construction

A 2-kb genomic DNA fragment from the K-ras proto-oncogene was subclonedinto an Apr-1-neo vector in both sense and antisense orientation. A 2-kbEco RI/Pst I fragment containing second and third exon sequencestogether with adjoining flanking intron sequences was isolated from theSP6 vector (Oncogene Sciences) and Klenow enzyme was used to make bluntends. Apr-1-neo vector was digested with Bam HI and blunt end ligationwas performed to obtain the Apr-1-neo AS or Apr-1-neo A constructs.

2. DNA Transfections

H460a or H322a cells were electroporated with 10 ug of Apr-1-neo AS orApr-1-neo S plasmid DNA. Forty-eight hours after transfection G418 wasadded into the medium at a concentration of 300 μg/ml for H460a and 200μg/ml for H322a. Individual colonies were picked up and grown in culturefor further analysis.

3. Southern Blot Analysis

High molecular weight DNA was isolated and digested with Eco R1(Boehringer-Mannheim) (20 μg), and electrophoresed in 0.8% agarose gel,transferred onto a Gene Screen membrane (NEN) and hybridized with a P³²nick translated 2 kb genomic K-ras DNA probe.

4. Measurement of RNA Expression

Total cellular RNA was isolated from the cell lines (Chomczymsky, etal., 1987). Twenty microgram of total RNA was size fractionated inMOPS/formaldehyde gel, transferred onto a Gene Screen membrane andprocessed for hybridization with riboprobes. A 302 bp genomic DNA of theK-ras gene was amplified by PCR spanning the third exon and intronsequences and was subcloned into a bluescript vector. In vitro S and ASRNA probes were synthesized using either a T7 or T3 promotor.

5. Polymerase Chain Reaction

Polymerase chain reactions were performed as previously described usingTaq 1 DNA polymerase (Saiki, et al., 1985). Oligonucleotide primerscorresponding to region the 5′ and 3′ regions of codons 12 and 61 ofhuman K-ras, H-ras, and N-ras genes were synthesized. Two micrograms ofgenomic DNA was subjected to 35 cycles of amplification. DNA sequencesof oligonucleotide primers used for PCR amplification are listed belowin Table 1.

TABLE 1 Primers Sequence Target KA61 5′ TTC CTA CAG GAA GCA AGT AGT A 3′K-ras 2nd exon KB61 5′ ACA CAA AGA AAG CCC DCC CCA 3′ KA12 5′ GAC TGAATA TAA SCT TGT GG 3′ K-ras 1st & 2nd exon KB61 5′ ACA CAA AGA AAG CCCDCC CCA 3′ HA12 5′ GAC GGA ATA TAA GCT GGT GG 3′ H-ras 1st & 2nd exonHB61 5′ CGC ATG TAC TGG TCC CGC AT 3′ NA12 5′ GSC TGA GTA CAA ACT GGT GG3′ N-ras 1st & 2nd exon NB61 5′ ATA CAC AGA GGA AGC CTT CG 3′

Primer KA61 corresponds to SEQ ID NO:1, primer KB61 corresponds to SEQID NO:2, primer KA12 corresponds to SEQ ID NO:3, primer HA12 correspondsto SEQ ID NO:4, primer HB61 corresponds to SEQ ID NO:5, primer NA12corresponds to SEQ ID NO:6, primer NB61 corresponds to SEQ ID NO:7.

6. Slot Blot Oligonucleotide Hybridization

PCR amplified DNA samples (12.5, 25, 50 ng) were blotted onto a GeneScreen membrane using a slot blot apparatus (Schleicher & Schuell). Thefilters were prehybridized and hybridized at 55° C. in 6×SSC, 5×Denhardts and 100 μg/ml of salmon sperm DNA for 2 h. Filters were washedtwice in 6×SSPE at room temperature and once for 30 mins at 58° C.Finally, blots were washed for 5 mins at 64° C. The filters were exposedto x-ray film for 12–24 h at −80° C.

7. Direct sequencing of PCR Amplified DNAs

PCR DNA corresponding to the second exon was purified in 8%polyacrylamide gel. A single DNA band was excised and purified DNA wasused for asymmetric amplification in 100 μl of PCR reaction mixture. One(KA 61) amplimer was added to this mixture. After 20 cycles,single-stranded DNA was purified through gene clean (Bio 101) and DNAwas eluted in 15 μl of water. Four microliters of DNA were mixed with 4μl of 10× Taq 1 buffer and 1 μl (10 pmol) of a second amplimer (KB 61)was used as a sequencing primer and DNA was sequenced using a sequenasekit.

8. RNA PCR Analysis

cDNA synthesis was carried out in a total volume of 20 μl containing 5μg of total RNA and oligo (dT) as a primer (Becker-Andre, et al., 1989).A portion of the cDNA corresponding to the first and second exons wasamplified to monitor the level of endogenous K-ras mRNA (FIG. 2A) usingKA12 and KB61 amplimers. Denaturation, annealing, and extension weredone at 92° C. for 1 min, 51° C. for 1 min and 74° C. for 1 min,respectively. However, annealing temperatures for N-ras and H-ras were44° C. and 42° C., respectively. In addition, two amplimers were alsoused in the same reaction mixture to amplify a 118-bp fragment of thep53 gene as an internal control. PCR products were either transferredonto a membrane and hybridized with ³²P labelled cDNA probe oralternatively, there were directly labelled during the last cycle ofamplification by adding 1 uCi of ³²P dCTP. The labelled PCR productswere loaded on an 8% nondenaturing polyacrylamide gel. The gel wasphotographed after ethidium bromide staining, dried, and exposed tox-ray film overnight at −80° C.

9. Western Blot Analysis of RAS Protein

Protein extracts were prepared by lysing cell in TBS (10 mM TRIS ph 7.5,100 mM Nacl, 1 mM PMSF 1% NP40, 1% deoxycholate. The extracts werecleaned by centrifugation at 10,000×g for 1 h. The protein concentrationof the supernatant was calculated spectrophotometrically. Five hundredmicrograms of protein were size fractionated in 12.55% SDSpolyacrylamide gel and electroblotted onto nitrocellulose membranes. Rasspecific p21 protein was detected using either K-ras or pan ras specificmonoclonal antibody (Oncogene Sciences) followed by ¹²⁵I-labelled goatanti-mouse second antibody.

10. Tumorigenicity in Nude Mice

The tumorigenicity of these cell lines was examined by subcutaneousinoculation of 10⁵ (FIG. 3B) and 10⁶ cells in nu/nu mice. Each cell linewas injected into 5 animals. Tumors were measured with linear calipersin 2 orthogonal directions by the same observer.

C. Results and Discussion

Segments of the K-ras gene containing first and second exons wereamplified from a number of NSCLC cell line DNAs by polymerase chainreaction (Saiki, et al, 1985) and subsequently hybridized with a set of³²P-labelled oligonucleotide probes (FIGS. 1A–1 & 2). Mutations wereconfirmed by a direct PCR DNA sequencing method. A homozygous mutationat codon 61 was detected in the NCI-H460A large cell undifferentiatedNSCLC cell line with a normal glutamine residue (CAA) substituted byhistidine (CAT). This cell line is highly tumorigenic in nude mice.

A recombinant plasmid clone was constructed using a wild-type 2 kb K-rasgenomic DNA segment carrying second and third exons together withflanking intron sequences subcloned into an Apr-1-neo expression vector(Gunning, et al., 1984) in the antisense orientation (AS; FIG. 1G).Sense orientation (S) plasmid constructs were used as a control (FIG.1B). AS or S K-ras RNA synthesis was accomplished by transfecting H460acells, a cloned derivative of the NCI-H460A cell line, with Apr-1-neo ASor Apr-1-neo S constructs by electroporation. The β-actin promoter ofthe vector was constitutively capable of directing the synthesis of RNAfrom the inserted DNA. The Apr-1-neo vector offered suitable G418 markergene expression for selection of the transfectants.

Individual G418 resistant colonies were selected and grown in culturefor further analysis. Stable integration of the plasmid DNA in thetransfectants was examined by Southern hybridization with a 2 kb DNAinsert from the original plasmid clone as a probe (FIG. 1C). Thesouthern blot analysis showed a single 3 kb Eco RI band corresponding tothe endogenous K-ras gene in the parental H460a cell line, butadditional bands were observed in the individual clones indicatingsingle or multiple copy inserts.

The extent of stable AS RNA expression and its effect on the endogenousK-ras mRNA level was investigated. Total RNA was extracted fromsubconfluent, growing cultures (Gunning, et al., 1987). The presence ofAS and S RNA was detected by northern blot hybridization using either anS or AS RNA probe synthesized in vitro from a Bluescript vector carryinga 302 bp K-ras DNA insert corresponding to the third exon and part ofthe intron sequences (FIG. 1D). Interestingly, the clones carrying theApr-1-neo AS vector show one RNA band at about 1.5 kb, but the cellscarrying the S construct show two RNA species. The reason for this isunknown, but the possibility exists that the RNA synthesized from thegenomic DNA under control of the β-actin promoter could be processed invivo. However, no corresponding hybridization band was detected in H460acells, which indicated a significantly higher level of K-ras RNA wassynthesized under the β-actin promoter.

Next, the p21 protein level in these transfectants was analyzed bywestern blot analysis (FIGS. 1E, F). A K-ras-specific p21 monoclonalantibody (Oncogene Science) was used to determine the level of K-rasprotein in transfectants, parental H460a cells, and Calu-1 cells, whichhave a high level of K-ras gene expression (FIG. 1E). Western blotanalysis showed a 95% reduction in K-ras p21 protein synthesis in theclones expressing the AS RNA, while parental cells, S K-ras clones, andCalu-1 cells showed a significant level of K-ras p21 protein. Theseresults indicate that AS RNA can effectively block the synthesis ofK-ras specific protein. Since members of the ras gene family share agreat deal of sequence homology and code for a similar p21 ras protein,we examined the total ras protein product in these clones was examinedusing a PAN ras monoclonal antibody (New England Nuclear) to determinewhether a reduced level of K-ras protein reflects any change in H-rasand N-ras p21 protein synthesis (FIG. 1F). Western blot analysisrevealed only a slight decrease in overall ras protein level in allclones containing Apr-1-neo-AS, as compared to 460a parental cells.

The effect of AS RNA on the specific production of mature endogenousK-ras mRNA was analyzed by cDNA PCR (FIG. 2). cDNA synthesized from thetotal RNA (Chomczymsky, et al., 1987) was subjected to PCR amplificationusing amplimers corresponding to the 5′-end of the first exon and the3′-end of the second exon (FIG. 2A). Because the AS RNA was generatedonly from a second and third exon of the K-ras gene, PCR amplified cDNArepresented the level of endogenous K-ras mRNA. A 246-bp amplified DNAfragment was labelled by ³²P dCTP and subsequently analyzed bypolyacrylamide gel electrophoresis. In addition, a 118-bp segment ofendogenous p53 cDNA was co-amplified in the same reaction mixture usingp53 specific amplimers to serve as an internal control for the PCR.

Results showed that H460a cells, clones expressing S RNA, and the Calu-1cell line expressed K-ras mRNA, as evidenced by the presence of a highlevel of amplification of the 246-bp cDNA product (FIG. 2B). H460aclones expressing AS RNA showed very little amplification, and cellularK-ras mRNA synthesis appeared to be completely inhibited (FIG. 2B, lanes5 and 6). In contrast, the endogenous p53 expression remainedunaffected. This prompted us to investigate the level of expression forother ras genes in these clones. We employed the same cDNA PCRmethodology to analyze the N-ras and H-ras mRNA level using N-ras andH-ras-specific oligonucleotides as amplimers. A steady state level ofH-ras and N-ras gene expression was observed, but no obvious changeeither in Apr-1-neo AS or Apr-1-neo S transfectants was noticed (FIGS.2C, D). The p53 gene expression serving as a control in theseexperiments remained unaffected. Thus, inhibition of K-ras expression byour AS RNA construct is specific.

H460a clones expressing AS K-ras RNA continued to grow in culture.However, H460a Apr-1-neo AS transfectants showed a three-fold reductionin growth, compared to the H460a Apr-1-neo-S transfectants and theparental H460a cells (FIG. 3A). The H322 NSCLC cell lung cancer cellline has wild-type ras family genes. H322 Apr-1-neo AS and Apr-1-neo Stransfectants had identical growth characteristics, indicating thatinhibition of wild-type K-ras is not sufficient to alter tumor cellgrowth rate. These results together indicate that the presence of senseK-ras RNA did not alter the growth kinetics of H460a cells. However, themarked growth retardation of the K-ras Apr-1-neo-AS transfectantssuggests that the mutated p21 protein contributes to the faster growthrate of these cells.

The tumorigenicity of cell lines expressing AS RNA was assessed bysubcutaneous injection of 10⁵ and 10⁶ cells in nu/nu mice. Subcutaneousinoculation of H460a cells at both doses led to the formation of tumorsin 15 days in all mice (3 to 5 mice per group in 3 separateexperiments). No tumor developed in mice injected with 10⁵ cells forboth clones of H460a AS cells during 120 days of observation in a totalof ten mice, whereas all mice receiving H460a cells developed tumors.When the inoculum was increased to 10⁶ cells, tumors grew in all mice,but the tumors in mice receiving AS clones grew at a slower rate thanH460a cells or the S control (FIG. 3B). Tumors were excised and analyzedfor K-ras expression by cDNA-PCR. K-ras expression was not detected intumors arising from injection of AS clones but was present in S clonesand H460a tumors.

The above experiments indicate that in H460a cells engineered tosynthesize AS K-ras RNA, the level of K-ras mRNA and K-ras p21 proteinare effectively down regulated. Reduction in the expression of K-rasmutated gene reproducibly reduced the rate of tumor growth in nu/numice. Our studies show that a construct can be made that distinguishesamong members of the ras family. Previous studies with ASoligonucleotides showed inhibition of p21 expression which led to celldeath (Brown, et al., 1989; Debus, et al., 1990). Our data indicate thatAS RNA generated from the genomic DNA of the K-ras gene can specificallyinhibit K-ras expression. In our model inhibition of activated K-rasreduced the growth rate of the H460a cells. However, there was no effecton cell viability or continued growth in culture. This suggests thatredundancy in p21 expression may compensate for absence of expression byone member of this family so that functions essential for maintenance ofcell viability are preserved. However, tumorigenicity was maintained inthe absence of activated K-ras expression although the rate of tumorgrowth was diminished. We hypothesize that in human NSCLC, ras mutationsconfer a growth advantage to the malignant cell.

EXAMPLE II Retroviral Vector-Mediated Transduction of K-ras AntisenseRNA into Human Lung Cancer Cells Inhibits Expression of the MalignantPhenotype

In overview, the present example illustrates a retroviral vector systemthat was developed by the inventors to efficiently transduce K-rasantisense constructs into human cancer cells. The 1.8-Kb K-ras genefragment DNA in antisense (AS) orientation to a β-actin promoter wasinserted into retroviral vector LNSX in two different orientations. Theconstructs were transfected into amphotropic packaging cell lineGP+envAm12 followed by alternating infection between the ecotropicpackaging cell line Ψ2 and GP+envAm12. Titers up to 9×10⁶ CFU/ml wereachieved without detectable replication-competent virus being produced.The human large cell lung carcinoma cell line H460a, which has ahomozygous codon 61 K-ras mutation, was transduced, and a transductionefficiency of 95% was obtained after 5 to 7 repeated infections.

DNA polymerase chain reaction analysis showed that the retroviralconstruct was integrated into the genome of H460a cells. K-ras antisenseRNA expression was detected in the cells by slot blot hybridization witha specific oligonucleotide probe. Translation of the mutated K-ras p21protein RNA was specifically inhibited, whereas expression of other p21species was unchanged. Proliferation of H460a cells was suppressedtenfold following transduction by LNSX-AS-K-ras. Colony formation insoft agarose and tumorigenicity in an orthotopic nu/nu mouse model weredramatically decreased in H460a cells expressing antisense K-ras.

A. Materials and Methods

1. Cells and Culture Conditions

NIH-3T3 cells, the human fibroblast cell line MRC-9, and ecotropicretrovirus packaging cell line Ψ2 (Mann et al., 1983) were grown inDulbecco-modified Eagle's Medium (DMEM; GIBCO) with a high glucosecontent (4.5 g/l) supplemented with 10% fetal bovine serum (SigmaChemical Co.). The amphotropic retrovirus packaging cell line GP+envAm12[(Markowitz et al., 1988); a gift from Dr. Arthur Bank] was grown inDMEM with high glucose; 10% newborn calf serum; 15 μg/ml hypoxanthine,250 μg/ml xanthine, and 25 μg/ml mycophenolic acid (HXM medium); and 200μg/ml hygromycin B (Sigma Chemical Co.). Non-small cell lung cancer cell(NSCLC) line H460a was maintained in RPMI 1640 medium with 5% fetalbovine serum (Mukhopadhyay et al., 1991). All cells were alsosupplemented with 2 Mm L-glutamine and antibiotics. The H460a wasestablished in culture from a human large cell undifferentiatednon-small cell lung cancer. This cell line has a homozygous codon 61K-ras mutation (Mukhopadhyay et al., 1991). The MRC-9 cell line has noevidence of mutations at codon 12 or 61 of the K-ras gene by singlestrand conformation polymorphism (SSCP) analysis and chain terminationsequencing.

2. Retroviral Vector Construction

Retroviral vector LNSX contains the selectable neo gene and a uniquecloning site for cDNA insertion. The neo gene is expressed from theretroviral long-term repeat (LTR), and the inserted gene has the simianvirus 40 (SV4 early promoter (Miller et al., 1989). A recombinantplasmid clone was constructed using a wild-type 2-Kb genomic DNA segmentcarrying second and third exons together with flanking intron sequencessubcloned into an Apr-1-neo expression vector in the antisenseorientation with a β-actin promoter (Mukhopadhyay et al., 1991). The5.8-Kb EcoR I/Nde I fragment of β-actin K-ras antisense was isolatedfrom this plasmid, and Klenow enzyme was used to blunt the ends. Toobtain the recombinant constructs in two different orientations (a andb) relative to the SV40 promoter (FIG. 4A), the LNSX retroviral vectorwas digested with Stu I (orientation a) or Hind III (orientation b) andblunt end ligation or Hind III linker ligation was performed. E. colibacteria were transformed by this recombinant plasmid DNA, and cloneswere screened by enzyme analysis. Southern hybridization with the 1.8-Kb³²P-nick-translated genomic K-ras DNA fragment probe was used to confirmthe construction of the positive clones using the followinghybridization condition: 6×SSC, 10× Denhart's solution, 0.1% sodiumdodecyl sulfate (SDS), 100 μg/ml salmon sperm DNA, and 25 Mm NaH₂PO₄ for2.5 h at 65° C.

3. Virus Production and Infection Efficiency

Amphotropic packaging cell line GP+envAm12 was transfected withrecombinant β-actin K-ras antisense LNSX plasmid DNA by the calciumphosphate co-precipitation method (Graham et al., 1973). Forty-eighthours later, the transfected cells were placed in medium containing G418(400 μg/ml). Colonies of “producer cells” were selected 10–14 d laterand expanded into large cultures.

The viral titer was tested by infecting NIH-3T3 cells. Plates (60 mm)were each seeded with 5×10⁵ NIH-3T3 cells. After 24 h, the medium onthese plates was replaced with 1 ml of serial dilutions of mediumconditioned for 24 h by confluent cultures of producer cells. Polybrenewas added to a final concentration of 8 μg/ml. The cells were incubated2–4 h and then 4 ml of fresh medium was added. Forty-eight h after theinfection, the infected cells were trypsinized and replated onto 100-mmtissue-culture dishes in medium containing 400 μg/ml G418. Coloniescould be counted 10–14 d later.

The high-titer GP+envAm12 cells transfected by α-actin K-ras antisenseLNSX (orientation a) were mixed with ecotropic packaging cell line Ψ2 ata ratio of 1:1. A total of 5×10⁵ cells from this mixture was seeded onto100-mm plates and passaged continuously for 1 month. These cells werethen selected by HXM medium (containing 200 μg/ml hygromycin B and 400μg/ml G418) for 10–14 d. The amplification of retrovirus production wastested by infecting NIH-3T3 cells. Supernatants from NIH-3T3 cellsinfected by GP+envAm12-producing cells and selected with 400 μg/ml G418for 10–14 d (short-term assay) or passaged continuously for 1 monthwithout G418 selection (long-term assay) were used to infect freshNIH-3T3 cells to detect the existence of replication-competentretrovirus.

NSCLC cell line H460a was infected once by incubating 10⁵ cells in6-well plates with 1 ml of each serial dilution (1:1, 1:10, 1:100,1:1000) of recombinant LNSX-antisense (orientation a) retroviral stockin the presence of 8 μg/ml polybrene. In another assay, 10⁴ H460a cellswere incubated with 0.5 ml LNSX-antisense (orientation a) retroviralstock (virus titer: 2×10⁶ CFU/ml) in 12-well plates, and 8 μg/mlpolybrene was added. The retroviral supernatant was added daily,following removal of medium and washing of the cultured cells, for 1–7d. Control cultures were incubated with fresh medium. Two days afterthese infections were completed, equal numbers of H460a cells wereseeded into a selective medium containing 300 μg/ml G418 or nonselectivemedium for 10–14 d. The infection efficiency for an infected cellpopulation was measured by dividing the number of G418-resistantcolonies by the number of colonies growing in the absence of selection.

4. PCR Analysis of Genomic DNA from Transduced H460a Cells

Genomic DNA was isolated by SDS-proteinase K lysis of H460a cellsfollowed by phenol-chloroform extraction. One microgram of genomic DNAwas placed in a total volume of 100 μl containing 50 Mm KCl, 10 MmTris-Hcl, 1.5 Mm MgCl₂, 0.1% gelatin, 20 Mm deoxyribonucleosidetriphosphates, 660 ng each of two neomycin phosphotransferase (neo-r)oligonucleotide primers (neo 1: CAAGATGGATTGCACGCACGCAGG; (SEQ ID NO:8)neo 5: CCCGCTCAGAAGAACTCGTC) (SEQ ID NO:9), and 2.5 units of Taq DNApolymerase. The tubes were cycled 35 times through 94° C. for 1 min, 50°C. for 1 min, and 72° C. for 2 min. The PCR products (15 μl) wereelectrophoresed on 2% gel (1% agarose, 1% nusieve GTG agarose) stainedwith ethidium bromide. The DNA was transferred onto a nitrocellulosemembrane and hybridized with ³²P-nick translated neo gene probe (HindIII/Sma I neo gene fragment of Psv2-neo plasmid DNA) in 6×SSC, 10×Denhart's solution, 0.1% SDS, 100 μg/ml salmon sperm DNA, and 25 MmNaH₂PO₄ at 65° C. for 3 h.

5. Slot Blot Hybridization of Poly(A⁺) RNA

Poly(A⁺) RNA was isolated from the cell lines. The RNA was denaturedwith 50% formamide, 6% formaldehyde, and 1×SSC at 68° C. for 15 min,then blotted onto nitrocellulose membranes (8 μg, 4 μg, or 2 μg) using aslot blot apparatus. The filters were prehybridized and hybridized at64° C. for 8–12 h with a ³²P-end-labeled 42-bp K-ras exon 2 DNAoligonucleotide probe in 1×SSPE, 2× Denhardt's solution, 1% nonfat drymilk, 10% dextran sulfate, 2% SDS, 200 μg/ml salmon sperm DNA, 200 μg/mlyeast tRNA, and 200 μg/ml polyadenylic acid. They were then washed twicein 1×SSPE, four times in 0.2×SSPE for 30 min at room temperature, andfinally with 0.1×SSPE for 30 min to 1 h at 47⁻58° C. The filters wereexposed for 2–3 d at 80° C. A β-actin probe was used to reprobe thefilters to confirm equal loading of RNA.

6. Immunoblot Analysis of ras Protein

Protein extracts were prepared by lysing cells in Laemmli buffer (130 MmTris-Hcl, Ph 6.8; 2% SDS; 10% glycerol). The extracts were boiled for 5min, cooled in ice and cleared by centrifugation at 10,000×g for 15 min.The protein concentrations were calculated by bovine serum albuminprotein assay. One hundred micrograms of protein was size-fractionatedby 12.5% SDS-polyacrylamide gel and electroblotted onto nitrocellulosemembranes. ras-specific p21 protein was detected using either a K-ras ora pan-ras-specific p21 monoclonal antibody (Oncogene Science, Mahasset,N.Y.) followed by horseradish peroxidase-labeled goat anti-mouse secondantibody (Pierce, Rockford, Ill.). The change in K-ras p21 levels wasdetermined by measuring absorbance with a video densitometer (Model 620,Bio-Rad, Richmond, Calif.).

7. Proliferation and Soft Agarose Colony Formation by H460a Cells

Parental and infected H460a cells (10³/well) which were selected or notselected with 300 μg/ml G418 were seeded and grew in 12-well plates for7 d. Cells were harvested and counted at different days. Humanfibroblast cell line MRC-9 was used as a control. Aliquots of 5×10⁴cells were mixed with 0.35% agarose in RPMI 1640 medium and plated overa base layer of 0.7% agarose and culture medium hardened in 60-mmdishes. Colonies (>50 cells) were counted using a phase contrastmicroscope 10–14 d later.

8. Tumorigenicity of H460a Cells in Orthotopic Lung Cancer Model

A model of orthotopic lung cancer growth in nu/nu mice was used tomeasure tumorigenicity of these cells. Balb/c nu/nu mice were irradiatedwith 350 Cgy of whole-body irradiation from a ⁶⁰Co source at 127cGy/min. After being anesthetized with methoxyflurane, theH460a-antisense-LNSX construct, the H460a cells infected by theretroviral vector alone, or H460a parental cells were injectedendotracheally (10⁵/mouse) using a 27-gauge blunt needle. Themediastinal block was harvested after 4 wk and tumor growth was measuredwith linear calipers in two orthogonal directions without knowledge ofthe animal treatment group.

B. Results

1. Construction and Generation of β-actin K-ras Antisense LNSXReplication-Defective Retrovirus

Recombinant plasmid clones were constructed by subcloning a wild-type1.8-Kb K-ras genomic DNA segment carrying second and third exonstogether with flanking intron sequences and a β-actin promoter inantisense orientation into an LNSX retrovirus vector in two orientations(FIG. 4). The plasmid DNA was analyzed by restriction enzyme mappingwith controls of LNSX plasmid DNA only and the β-actin K-ras antisenseApr-1-neo vector. β-actin K-ras antisense LNSX was constructed in twodifferent orientations, both of which included the 4-Kb β-actinpromotor, the 1.8-Kb K-ras fragment, and a 6-Kb LNSX vector fragment.The digested DNA was transferred to a nitrocellulose membrane andhybridized with a 1.8-Kb ³²P-nick-translated genomic K-ras probe.Orientation a has the K-ras 5′ end adjacent to the SV40 promoter of LNSXand thus is placed in a reverse orientation((LTR_neo_SV40_K-ras_β-actin_LTR). Orientation b has the α-actinpromoter adjacent to the SV40 promoter (LTR_neo_SV40_β-actin_K-ras_LTR).

The amphotropic retrovirus was produced by transfection of theGP+envAm12 packaging cell line with this recombinant DNA. To increaserecombinant retrovirus production, amphotropic β-actin K-ras antisenseLNSX (orientation a) GP+envAm12 cells were co-cultivated with ecotropicΨ-2 for 1 month. This mixed-cell pool was selected by HXM medium withhygromycin B and G418. The highest viral titer generated by testing theselected colonies was 9×10⁶ CFU as determined by transduction andselection of NIH-3T3 cells.

Replication-competent virus produced by GP+envAm12 was measured byinfection of fresh NIH-3T3 cells with medium conditioned in NIH-3T3 cellcultures infected by recombinant retrovirus and selected by G418 for10–14 d (short-term assay). In a more sensitive long-term assay, NIH-3T3cells were infected with the medium conditioned by GP+envAm12-producingcells, after which they were passaged for 1 month to allow for thespread and amplification of a rare recombinant wild-type virus in theculture. Medium collected from these NIH-3T3 cells was used to infectfresh NIH-3T3 cells. Both the short-term and long-term assays showedthat no detectable replication-competent retrovirus was produced byGP+envAm12 cells.

2. Infection Efficiency in H460a Cells.

H460a cells were infected with recombinant LNSX-antisense retrovirus byincubating with viral stocks in the presence of 8 μg/ml polybrene. Theinfection efficiencies of H460a cells at varying virus to H460a cellsratios (V/T) of 1:10, 1:1, 10:1, and 100:1 were 7.5±1%, 26±1.2%, 53±11%,and 57±13% after a single cycle of infection (FIG. 5A). The efficiencyincreased with higher V/T ratios and plateaued at the 10:1 V/T ratio.The infection efficiency increased also with the number of infectionexposures at the same V/T ratio (100:1) (FIG. 5B). Infectionefficiencies of 97±15% and 25±2.6% were achieved after five cycles ofinfection of H460a cells at 10:1 and 1:10 V/T ratios, respectively.

3. Detection of Transduced neo Gene by PCR in Infected H460a Cells

Genomic DNA was isolated and amplified by PCR with neo 1 and neo 5oligonucleotide primers. A 790-bp segment of the neo gene was detectedin transduced H460a cells, but not in parental H460a cells (FIG. 6A).Southern hybridization with a ³²P-nick-translated neo gene probeconfirmed the identity of the neo gene band (FIG. 6B), indicating thatthe inserted retrovirus gene was successfully integrated into H460agenomic DNA.

4. Expression of K-ras Antisense RNA and Specific Inhibition of K-rasProtein p21 in H460a Cells

Poly(A⁺) RNA was extracted from parental and infected H460a cells. Theexpression of K-ras antisense RNA was detected by slot blothybridization with a 42 bp K-ras exon 2 oligonucleotide probe (FIG. 7).The level of expression of K-ras antisense RNA in H460a cells infectedby the orientation (a) retrovirus was higher than that of H460a cellsinfected by the orientation (b) retrovirus. Reprobing the filter withthe β-actin DNA probe showed that each sample was loaded equally.

The inventors next analyzed the p21 protein level in these H460a cellsby immunoblot analysis. A K-ras-specific p21 monoclonal antibody wasused to determine the level of K-ras protein in parental and infectedH460a cells. K-ras p21 protein synthesis was reduced by 90% in the H460acells expressing high levels of K-ras antisense RNA (orientation aretrovirus) and by 30% in the H460a cells infected with orientation bretrovirus, compared with those of parental H460a cells and H460a cellsinfected only by the LNSX vector retrovirus (FIG. 8A). The total rasprotein production in these cells was also examined, using a pan-rasmonoclonal antibody, to determine whether a reduced level of K-rasprotein reflected any change in H-ras and N-ras p21 protein synthesis.The western blot analysis revealed that overall ras protein levels inall infected cells were only slightly decreased from the level in H460aparental cells (FIG. 8B).

5. Suppression of H460a Cells' Growth In Vitro and Colony Formation inSoft Agarose

H460a cells expressing K-ras antisense RNA continued to be viable inculture. However, growth of H460a cells expressing high levels of K-rasantisense RNA (orientation a) was reduced compared with that of H460acells infected with LNSX vector only and parental H460a cells (FIG. 9A).Transduction of the human lung fibroblast cell line MRC-9, which has awildtype K-ras gene, with LNSX and LNSX-AS-K-ras (a) did not affectproliferation of that cell line (FIG. 9B). Previous studies have shownthat expression of the 1.8-Kb K-ras fragment in the sense orientationdoes not affect proliferation or tumorigenicity of H460a cells(Mukhopadhyay et al., 1991).

The effect of K-ras antisense RNA expression on the growth of softagarose colonies of H460a cell lines was determined. Colony formation insoft agarose was dramatically decreased in H460a cells expressing K-rasantisense RNA (number of colonies, orientation a: 135±26; orientation b:320±37) as compared with parental H460a cell line (1096±434) and H460acells infected only with retroviral vector LNSX (1048±322) (FIG. 10).

6. Suppression of Tumorigenicity in an Orthotopic Lung Cancer nu/nuMouse Model

Intratracheal inoculation of H460a cells in irradiated nu/nu miceresulted in the growth of endobronchial tumors with mediastinalextension in >80% of the mice after 4 wk. Twelve of 14 mice inoculatedwith parental H460a cells and seven of nine mice inoculated with H460acells infected with the LNSX vector developed tumors (Table 2). Three ofseven mice inoculated with H460a cells transduced with theLNSX-AS-K-ras(b) had tumors. Cells expressing the highest level ofAS-K-ras with the greatest reduction in p21 expression had the lowestincidence of tumor formation. Only three of 17 mice receivingH460a-LNSX-AS-K-ras(a) cells had tumors and the volume of these tumorswas much less than tumors in the control groups. Statistical analysis(chi-square) shows that there is a statistically significant difference(p<0.005) in tumorigenicity between H460a-LNSX-AS-K-ras(a) and thecontrol groups.

TABLE 2 Tumorigenicity of H460a in orthotopic nude mice model Mice withMean Cell lines Cells injected Tumors (%) volume(mm³)¹ H460a 10⁵ 12/14(86) 39.9 ± 4.25 H460a-LNSX 10⁵ 7/9 (78) 12.5 ± 2.2 H460a-LNSX-AS-K- 10⁵3/17² (18) 2.95 ± 1.25 ras(a) H460a-LNSX-AS-K- 10⁵ 3/7 (43) 1.74 ± 1.5ras(b) Note: The irradiated (350 Cgy) nude mice were inoculated with 10⁵H460a cells intratracheally. Tumors were measured after 30 days. ¹Meanvolume based only on mice with tumors. ²p < .005 compared to H460a andH460a-LNSX by χ² analysisB. Discussion

A retroviral vector-mediated gene transfer system was developed tointroduce a partial K-ras genomic sequence into lung cancer cell lineH460a, which has the K-ras gene mutation at codon 61. The K-ras sequencecarries second and third exons together with flanking intron sequencesand a β-actin promoter in antisense orientation. The transduced K-rasantisense gene was integrated and efficiently expressed in H460a cells.For H460a cells expressing AS-K-ras, K-ras-specific p21 proteinexpression was reduced more than 90%, whereas the total ras proteinproduction decreased only slightly relative to the control group(parental H460a cells and those infected only by the retroviral vector).Specific inhibition of oncogene (e.g.,N-ras, H-ras) expression byantisense oligonucleotides has been reported by a few laboratories, butthe short biological half-life and low transfer efficiency ofoligonucleotides in the cell were problems in those studies(Saison-Behmoaras et al., 1991; Chang et al., 1991; Neckers et al.,1992).

In the presently disclosed retroviral gene transfer system, hightransfer efficiency, prolonged expression of K-ras antisense RNA, andinhibition of K-ras p21 protein were achieved, particularly through theuse of reverse orientation constructs. Cells expressing the antisenseK-ras construct have been grown in continuous culture for over 6 months.The expression of the neoplastic phenotype of the H460a cell line,including growth rate, ability to form colonies in soft agarose, andtumorigenicity in nude mice, were dramatically reduced. Previous studieshave shown that cancer cells often have multiple genetic alterations.Therapy directed toward oncogenes will be practical only if therapeuticeffects occur with targeting of one or two genes. In this case reversalof a single genetic lesion resulted in suppression of critical featuresof the malignant phenotype.

The inventors results indicate that the expression of the mutated K-rasprotein plays an important role in the oncogenesis and growth of cellline H460a. When human fibroblast cell line MRC-9 and NSCLC cell lineH322a, which has a wildtype K-ras gene, were infected by theLNSX-antisense retrovirus, the growth curves were not significantlydifferent from that of the control cells. Thus, this construct candistinguish among closely related members of the ras family. Continuedviability of cells expressing AS-K-ras suggests that other closelyrelated members of the ras family may subsume the function of K-ras.

It is unlikely that any therapy targeting oncogenes or their productswill be absolutely specific for cancer cells. If other genes cancompensate for loss of normal function by a specific oncogene mediatedby an antisense construct, the harmful effects of the therapy will bereduced. Additional support for this concept comes from a recent studyby Soriano and coworkers (Soriano et al., 1991) in which transgenic micewere created that lacked a functional c-src proto-oncogene. Theresulting developmental defect in the mice was osteopetrosis. Theubiquity of c-src, its high degree of conservation among species, andits role in mitosis suggest that inactivation would be lethal, but thiswas not the case; viable mice were recovered. A possible explanation isthat other closely related nonreceptor tyrosine kinases such as yes andfyn can compensate for loss of c-src.

Efficient transfer of constructs that can modify expression of oncogenesand tumor suppressor genes is critical to the analysis of the functionalrole of these genes and the potential therapeutic use of theseconstructs. We found that infection efficiency could achieve 97% using amultiple infection protocol. After one exposure, efficiency as high as57% was achieved at a 10:1 V/T ratio, with little additional increase inefficiency obtained by increasing the V/T ratio to 100:1, indicatingthat such factors as the quality of the virus preparation and theproliferation status of the H460a cells may affect the infectionefficiency. In the low V/T ratio (1:10) assay, infection efficiency ofabout 25% was obtained after five exposures. Ratios of retrovirus totumor cells or premalignant cells such as these are achievable withregional therapy in the setting of minimal residual cancer orpremalignant conditions. This revealed that, in the clinical setting,even if the high V/T ratio cannot be achieved, a satisfactory infectionefficiency may be obtained by multiple infection exposures. Not all thepatient's cancer cells will be in the proliferative stage at eachinfection exposure, and the retrovirus may selectively infect only theproliferating cells (Miller et al., 1990). Multiple exposures to theretrovirus can address this problem and maximize the number oftransduced tumor cells. The use of a promoter which is commonlyexpressed in epithelial cells may also contribute to efficientexpression in human cancer cells of epithelial origin.

The high titer (9×10⁶ CFU/ml) of the producer cell line was obtained by“ping-pong” infection between the amphotropic packaging cell lineGP+envAm12 and ecotropic packaging cell line Ψ-2. The titer was 100times more than those of cell lines produced by GP+envAm12 before“ping-pong” infection. A similar result was reported by Bodine et al.,but in their assay all of the high-titer cell lines after ping-ponginfection also produced replication-competent viruses (Bodine et al.,1990). In the present system, no detectable replication-competent viruswere produced even in the stringent long-term assay. This may be due tothe safety of GP+envAm12, in which the Moloney murine leukemia virusgag, pol gene, and 4070A amphotropic env gene are separated on Pgag-polgpt and PenvAm, two different plasmids, and the packaging signals and3′long-terminal repeats are removed. The three specific recombinationevents required to generate replication-competent viruses are unlikelyto occur in this system (Markowitz et al., 1988).

A very interesting finding is that, of the two orientations of theconstruct in the recombinant retroviral vectors[LTR_neo_SV40_K-ras_β-actin_LTR (a) and LTR_neo_SV40_β-actin K-ras_LTR(b)], the orientation (a) vector showed higher transfection efficiency,higher virus titer, and higher K-ras antisense RNA expressionefficiency. It is possible that the SV40 promoter may suppress theβ-actin promoter as described in other systems (Emerman et al., 1984).However, the SV40 promoter is not as active as the β-actin promoter, andtherefore this effect may have some degree of promoter specificity(Gunning et al., 1987; Emerman et al., 1986). If some sense transcriptswere produced by this promoter in orientation (a), the splicing of theintron sequence would render the transcripts unable to hybridize withthe antisense transcripts. The effectiveness in the reduction of K-rasp21 protein by orientation (a) supports the absence of this type ofinhibitory effect. Interestingly, the use of a β-actin promoter inorientation (b) with an LNL6 retrovirus yielded low rates of infectivityand low levels of gene expression (Owens et al., 1991).

According to the original “seed and soil” hypothesis proposed by Pagetin 1889, organ-site specific implantation of tumor cells is essentialfor optimal growth and progression of tumors in vivo (Paget, 1989). Thisconcept has been widely supported by numerous studies in metastatictumor models (Fidler, 1986) and, recently, athymic nude mice models havebeen used to study the orthotopic propagation of selected human solidtumors, including lung cancer (Howard et al., 1991). We successfullyused an intratracheal model for the orthotopic propagation of human lungcancer H460a cells in irradiated nude mice to assess the tumorigenicityof the transduced cells. The H460a cells grew well in the model, and thetumorigenicity of H460a cells expressing K-ras antisense RNA wasdramatically decreased. Further studies using retroviral vectors as aregional delivery method for K-ras antisense gene expression in vivo arein progress in our laboratory. The orthotopic in vivo model in useclosely resembles the clinical setting, allowing a further assessment ofthe feasibility of using the recombinant retrovirus therapeutically inlung cancer.

EXAMPLE III Clinical Protocol for Modification of Oncogene and TumorSuppressor Gene Expression in Non-Small Cell Lung Cancer

This example is provided to demonstrate a protocol for administering andassessing the efficacy and toxicity of the intralesional administrationof retroviral constructs containing antisense (AS) K-ras (for tumorswith mutated K-ras) and wildtype p53 (wtp53) (for tumors with mutated ordeleted p53) into residual endobronchial NSCLC which obstructs abronchus and which is refractory to conventional therapy.

A. Downregulation of Activated K-ras/ Expression with an AntisenseConstruct

1. Gene Construct

The retroviral vector construct contains the AS-K-ras fragment with itsβ-actin promoter inserted into the LNSX vector (Miller et al., 1989;Palmer et al., 1987). The orientation of the insert is such that thetranscription of the AS-K-ras is driven by the β-actin promoter in anorientation that is reverse with respect to transcription from theretroviral LTR.

2. Packaging

Because recombination events may lead to the production of areplication-competent virus, a safe and efficient amphotropic packagingcell line is necessary for transfer of exogenous genes into human cancercells. The packaging cell line employed is constructed so the gag-poland env genes are separated on two different plasmids (Markowitz et al.,1988). The packaging signals and 3′ LTRs have also been removed; thiswas done by transfection of NIH 3T3 cells by a plasmid containingMoloney murine leukemia virus gag and pol genes and a separate plasmidcontaining the env gene. The GP+envAM12 clone that produces high levelsof env protein was selected to be used as the packaging cell line. Thecombination of mutations for the two plasmids requires at least threerecombination events between the helper plasmids and the retroviralvector; the improbability of this sequence of events essentiallyeliminates the possibility of replication-competent virus production.The presence of functioning retroviral genes in the packaging cell linewill be monitored by an assay for reverse transcriptase production andby immunoprecipitation of env protein by metabolic labeling andimmunoprecipitation with anti-env antiserum (Markowitz et al., 1988).

Continued absence of infectious virus will be determined fromtransfection-infection experiments. A neo-containing vector will betransfected into GP+envAM12 cells; colonies will be selected with G418.The supernatants will be used to infect NIH 3T3 cells. Selection withG418 will be done after one month to ensure the survival of rarerecombinants that do not have the neo gene but subsequently infectneo-positive cells. Supernatants from the infected NIH 3T3 cells shouldnot be infectious. These secondary supernatants will be used to infectnaive NIH 3T3 cells. Lack of infectivity will indicate absence ofreplication competent virus.

A protocol for generating retroviral particles is as follows:

-   -   (1) GP+envAm12 cells are grown in Dulbecco's modified Eagle's        medium containing 10% newborn calf serum, 15 μg/ml hypoxanthine,        250 μg/ml xanthine, and 25 μg/ml mycophenolic acid and selected        in 200 μg/ml hygromycin.    -   (2) Vectors are transfected by electroporation.    -   (3) G418 (400 μg/ml) selection is begun 48 hr after transfection        and colonies are expanded 10 to 14 days later.    -   (4) The viral titer is tested by infecting NIH 3T3 cells. After        producer cells are semiconfluent, medium is replaced with        Dulbecco's modified Eagle's medium containing 10% newborn calf        serum but without G418. Cells are seeded at 5×10⁵ in 60-mm        dishes. The medium is removed 18 hr later, filtered (0.45        micron), and diluted serially (10² to 10⁷). One milliliter of        medium is applied to cells. Polybrene (8 μg/ml) is added. Cells        are incubated for 2 hr at 37°, and then 4 ml of fresh medium is        added.    -   (5) After 48 hr cells are replated onto 100 mm tissue culture        dishes and selected with G418. Previous human studies have used        the PA317 producer cell line. This cell line is preferred        because of the extensive experience with its use and prior        approval for human use.

4. Preclinical Studies

The 2 Kb K-ras fragment (genomic exons 2 and 3) with a β-actin promoterwas cloned into the LNSX retroviral vectors in both orientations. Thep53 cDNA with its β-actin promoter was cloned into the LNSX retroviralvectors in both orientations. Both the LNSX-AS-K-ras and theN2A-AS-K-ras have been successfully packaged in the GP+envAm12 packagingcell line. Initial titers ranged up to 10⁴. By using a “ping-pong”technique, the titer of the LNSX-AS-K-ras supernatant was increased to5×10⁶. In this technique, supernatants from the GP+envAm12 packagingcell line were used to transduce the ecotropic packaging cell line Ψ2(Mann et al., 1983). Supernatants from this transduction were used againto transduce GP+envAm12. Both constructs were then transduced into H460acells. Specific expression of K-ras AS RNA was shown by slot blotanalysis using vector only negative controls and a β-actin probe for aloading control. Western blotting studies showed that expression of theK-ras p21 protein was specifically reduced. Next the effect of multiplecycles of transduction on transduction efficiency was assessed.Transduction efficiency was assessed on a functional level (FIG. 11).H460a cells were transduced with either LNSX or LNSX-AS-K-ras daily for4 consecutive days. Cells grew for 7 days without selection.

The percent reduction in the growth fraction of the AS transduced cellsreflects the efficiency of transduction as growth of a selectedpopulation of AS transduced cells does not occur during this timeperiod. The growth of the unselected AS transduced cells was less than20% at 7 days. Thus, the simple manipulation of exposing cells to thepackaged retrovirus for 4 consecutive days caused a striking increase intransduction efficiency. In a subsequent experiment H460a cells weretransduced daily for 7 consecutive days with LNSX-AS-K-ras and thenselected for colony formation in G418 (FIG. 12). Colonies were comparedto H460a cells that were not exposed to selective medium. Followingselection the efficiency of colony formation by the transduced cells was98%. This reinfection strategy is applicable to regional therapy. Theapparent low toxicity of the retroviral constructs should permitmultiple treatments. It is anticipated that the residual number ofendobronchial tumor cells can be reduced to <10⁷ so that an excess ratioof retroviral particles to proliferating tumor cells can be achieved.

The tumorigenicity of the transduced H460a cells was studied in anorthotopic lung cancer model. Intratracheal inoculation of H460a cellsin irradiated (350cGy) nu/nu mice resulted in the growth ofendobronchial tumors with mediastinal extension in >80% of mice after 4weeks. The H460a-AS-LNSX, H460a-LNSX, and H460a cells (10⁵/mouse) wereinjected endotracheally and the mediastinal block was harvested after 4weeks. Mice were assessed for tumor growth without knowledge of thetreatment group. Seven of 9 mice inoculated with H460a-LNSX (mean volume12.5±2.2 SE mm³) and 12 of 14 mice inoculated with H460a parental cells(mean volume 39.9±4.25 SE mm³) had tumors. Only 3 of 17 mice receivingH460a-AS-LNSX cells had tumors (mean volume 2.95±1.25 mm³). From thesestudies, it is concluded that 1) retroviral gene transduction can beused to express anti-sense constructs in human tumor cells at levelsthat mediate a biologic effect; 2) AS-mediated inhibition of activatedK-ras expression effectively inhibits proliferation and tumorigenicityof human cancer cells. Expression of the AS-LNSX expression in the H460acells has been stable up to 6 months.

B. Restoration of Expression of wtp53 Gene Product

1. Preliminary Studies with Plasmid DNA

The p53 gene is the most commonly altered gene yet described in humancancers. To study this gene, a cell culture model system of cell linesvarying in p53 expression was established. The H322a lung adenocarcinomacell line expresses the mutant p53 protein as shown by the presence ofhigh levels of endogenous p53 mRNA and phosphorylated protein. We showedthat the H322a cell line has a G:T transversion at codon 248 (Arg toLeu) with absence of the wildtype allele. The H358a cell line has ahomozygous p53 deletion. The H460a and H226b cell lines are homozygousfor the wildtype p53. Expression vectors for sense (S-p53) and antisensep53 (AS-p53) cDNA with a β-actin promoter were constructed to study theeffect of wtp53 expressed in lung cancer cells with mutant or deletedp53 and the effects of reducing wildtype and mutant p53expression.(Mukhopadhyay et al., 1991)

Stable transfectants of p53 mutant cells (H322a) or deleted p53 (H358)expressing S-p53 could not be rescued. Failure to isolate coloniesexpressing sense p53 RNA in cells with homozygous mutant or deletedalleles shows that wtp53 can suppress transformation in cancer cellsexpressing a mutant p53 or having a homozygous p53 deletion.

In general, transfection with AS-p53 reduced colony formation (10-fold)by cells with endogenous mutant p53. This indicates that expression ofmutant p53 contributes to the transformed phenotype. As expected, cellswith wtp53 (H226b) showed increased tumorigenicity when transfected withAS-p53. The H226b cells expressing AS-p53 grow significantly morerapidly in nu/nu mice than the cells transfected with the controlplasmid. This indicates that elimination of the wtp53 gene productenhances features of the malignant phenotype.

The inventors studies showed that wtp53 is dominant and can suppress themalignant phenotype in cells with mutant or deleted p53. The presence ofthe mutant p53 confers transforming potential to the gene product, whichcan be suppressed by AS-p53. Thus, in cancer cells both the absence ofwtp53 and the presence of certain p53 mutations may enhance themalignant phenotype.

2. Gene Construct

The retroviral vector construct contains p53 cDNA with its β-actinpromoter inserted into the LNSX vector (Miller et al., 1989; Palmer etal., 1987) in a reverse orientation, in essentially the same manner asdescribed for the p21 AS embodiments.

3. Packaging

See section A.2. above

4. Preclinical Studies

The LNSX-p53 and the DC-p53 were transduced into H322a (mutant p53),H358a (deleted p53), and H460a (wt p53). H322a cells that underwent onecycle of infection with the wtp53 construct but without G418 selectionhad an over 3-fold reduction in proliferation compared to cells thatreceived either the unmodified vector or no treatment. Two cycles oftransduction without G418 selection resulted in a 5-fold reduction inproliferation (FIG. 13). A similar result was observed for the H358acell line when transduced with LNSX-p53. The proliferation of the H460acell line which has a wildtype p53 was not altered by transduction withany of the p53 retroviral constructs (FIG. 14). Thus, retroviralmediated gene transfer of wtp53 into human lung cancer cells withdeleted or mutated p53 significantly reduces the proliferation of thosecells. The expression of the mutated p53 protein is uniform in culturedcell lines as detected by immunohistochemistry. In fresh lung tumorsthat express high levels of p53 protein, expression is detected in >90%of cells.

A critical question is the ability of the retroviral constructs totransduce established tumor cells in vivo. This question was addressedby injecting H460a (10⁵) cells in the mouse right mainstem bronchusfollowed 3 days later by lavage with LNSX retroviral supernatant (10⁶CFU in 0.1 ml). LNSX was used so that the neo gene could be used as amarker for transduction. It was necessary to recover tumor cells foranalysis so that the AS construct was not used. Tumors were harvestedand the presence of the neo gene was assessed by Southern hybridization.The neo gene was detected in the DNA from the H460a cells indicatingsuccessful transduction of the retrovirus 30 days after lavage. Althoughthis data is encouraging, the model has limitations. Direct injection ofendobronchial tumor is not possible in this model. Other sites of directinjection do not accurately simulate the milieu of endobronchial lungcancer. Thus, definitive answers concerning efficacy must be obtainedthrough this clinical trial.

C. Treatment Plans

In proposed preferred treatment protocols, patients will undergobronchoscopy to assess the degree of obstruction. As much gross tumor aspossible should be resected endoscopically. Patients should preferablyundergo bronchoscopy under topical or general anesthesia. A Stifcor™transbronchial aspiration needle (21 g) will be passed through thebiopsy channel of the bronchoscope. The residual tumor site will beinjected with 10⁷ CFU of the appropriate retroviral supernatant. Thevolume will be no greater than 10 ml. Protamine will be added at aconcentration of 5 μg/ml. This is 0.2% of the amount given intravenouslyto reverse heparinization.

Injections will be circumferential and will be intratumor andsubmucosal. The AS-K-ras supernatant will be used for K-ras mutationsand the p53 supernatant will be used for p53 mutations. The injectionswill be repeated daily for five consecutive days. The treatment will berepeated monthly.

1. Criteria for Response and Toxicity

There are various criteria that one should consider as presenting theexistence of a need for response or the existence of toxicity. To assistin determining the existence of toxicity, the tumor bed should bephotographed prior to a course of therapy. The longest diameter and itsperpendicular will be measured. Size will be reported as the product ofthe diameters. From these date, one can calculate from these numbers therate of regrowth of the tumor.

The time to progression can also be measured from the first observationwith reduction in tumor bulk until there is evidence of progressivedisease. Progressive Disease is defined as an increase of ≧25% in thesum of the products of the diameters of the measured lesion. Patientsmust have received at least two courses of therapy before a designationof progression is made. The survival of patients will be measured fromentry into protocol.

2. Potential Risks of Retroviral Gene Transduction

The possibility of causing malignancy in normal cells secondary torandom insertion of the retroviral vector in the genome exists althoughthis risk is thought to be very low. Tests of viral supernatant will beconducted to assure that no replication competent virus is present.Non-replicating bronchial epithelial cells will not take up the vector.

3. Risk from Murine Retrovirus.

The retrovirus derived from the Moloney murine leukemia virus ismodified so that it no longer contains intact viral genes. Thus, itcannot produce an intact infectious virus. Assays may be performed onthe retroviral vector supernatant and the packaging cell to insure thatreplication competent virus is not present. Extensive safety studieshave been performed on this retroviral construct in primates. Largeinfusions of infectious murine amphotrophic virus produce no acutepathologic effects. Primates have also received retroviral gene-modifiedautologous bone marrow cells with no evidence of toxicity as long as 4years after infusion.

4. Efficacy of Aminoglycoside Antibiotics.

The neomycin resistance gene product, neomycin phosphotransferase,phosphorylates the 3′ hydroxyl group of the aminohexose I of neomycinand its analogues. Amikacin, but not gentamicin and tobramycin which donot contain an hydroxyl at the 3″ position, is inactivated. Thus,induction of the neomycin resistance gene would not excludeaminoglycosides or any other conventional antibiotic from use in thesepatients.

5. Criteria for Discontinuing Therapy

There are various criteria that one should consider employing in makinga decision to discontinue therapy. For example, an increase in theendobronchial tumor after a minimum of 2 or more courses of therapy, orthe development of unacceptable toxicity defined as unpredictable,irreversible, or Grade 4. Patient refusal of therapy due to a specifictoxicity should be graded as 4 and an explanatory note recorded. Oneshould also consider discontinuing therapy upon the occurrence ofsignificant hemoptysis, coagulopathy, or progressive postobstructivepneumonia.

The present invention has been disclosed in terms of preferred modesfound to work well in the practice of the invention. However, numerousmodifications and changes in the steps, procedures used and materialwill become apparent to those of skill in the art in light of thedisclosure. All such modifications are intended to be within the spiritof the present invention and scope of the appended claims.

REFERENCES

The following references are hereby incorporated by reference to theextent that they describe, explain, teach methodology for or provideuseful materials or compositions for use in connection with the practiceof the present invention, for the reasons specified in the foregoingtext.

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1. A method for treating cancer in a human patient comprising directlyintroducing into a p53-deficient tumor cell of the patient a retroviralcomposition comprising a retroviral vector construct in apharmaceutically acceptable buffer, wherein said retroviral vectorconstruct comprises a wild-type p53 gene coding region, the codingregion being operatively linked to a promoter to effect expression ofthe coding region, wherein said expression is effective to inhibit thegrowth of said tumor cell.
 2. The method of claim 1, wherein the humanpatient has an epithelial cancer.
 3. The method of claim 2, wherein thehuman patient has lung cancer.
 4. The method of claim 3, wherein thepatient has non-small cell lung cancer.
 5. The method of claim 1,wherein the human patient is administered both a wild-type p53 genecoding region and an antisense K-ras gene coding region.
 6. The methodof claim 1, wherein the promoter and gene coding region are positionedin an orientation that is opposite that of retroviral transcription. 7.The method of claim 1, wherein the vector comprises a marker gene. 8.The method of claim 4, wherein the non-small cell lung cancer is sqamouscell cancer.
 9. The method of claim 4, wherein the non-small cell lungcancer is adenocarcinoma.
 10. The method of claim 4, wherein thenon-small cell lung cancer is large-cell undifferentiated.
 11. Themethod of claim 3, wherein the lung cancer is small cell lung cancer.12. The method of claim 1, wherein the promoter is selected from thegroup consisting of β-actin, CMV, RSV, N2A, LN, LNSX, LNSN, LNCX andSV40.
 13. The method of claim 12, wherein the promoter is β-actin. 14.The method of claim 12, wherein the promoter is CMV.
 15. The method ofclaim 1, wherein said introducing is via intratumoral injection.
 16. Themethod of claim 1, wherein said introducting is via circumferentialinjection of said tumor.
 17. The method of claim 1, further comprisingtumor resection.
 18. The method of claim 17, wherein said resection isvia bronchoscopy.
 19. The method of claim 17, wherein said introducingis via injection of a resected tumor site.
 20. The method of claim 16,wherein said injection is submucosal.
 21. The method of claim 16,wherein said injection is subcutaneous.
 22. The method of claim 1,wherein said introducing is regional.
 23. The method of claim 1, whereinsaid introducing is performed multiple times.
 24. The method of claim23, wherein said introducing is performed daily for five consecutivedays.
 25. The method of claim 23, wherein said introducing is performedmonthly.
 26. The method of claim 1, further comprising photographingsaid tumor mass prior to introducing said retroviral composition. 27.The method of claim 1, wherein said retroviral composition is deliveredin 10 ml.
 28. The method of claim 1, wherein said retroviral compositionis delivered in 0.1 ml.
 29. The method of claim 1, wherein saidretroviral composition has a titer of at least 10⁵ CFU/ml.
 30. Themethod of claim 29, wherein said retroviral composition has a titer ofat least 10⁶ CFU/ml.
 31. The method of claim 30, wherein said retroviralcomposition has a titer of at least 6×10⁶ CFU/ml.
 32. The method ofclaim 31, wherein said retroviral composition has a titer of at least9×10⁶ CFU/ml.
 33. The method of claim 1, wherein said retroviral vectoris derived from MMTV or MMLV.
 34. The method of claim 1, wherein saidtumor mass is endobronchial.
 35. The method of claim 1, wherein saidretroviral composition further comprises protamine.
 36. The method ofclaim 1, wherein said protamine is present at a concentration of 5μg/ml.
 37. The method of claim 1, further comprising removing tumorcells from said patient, introducing said retroviral composition ex vivoand returning retrovirally-treated cells to said patient.
 38. The methodof claim 37, wherein said tumor cells are bone marrow-derived.